schematics
I've seen some designs which have mounting hole included in the schematic. Are there any good reasons of doing that?
I can see one advantage of doing so when you want to connect your mounting holes to some nets (e.g. GND). But what if the holes aren't supposed to be connected to any net?
There are a number of uncertainties in what you say you are doing. You need to stabilize the patient and understand what is really going on in order to make progress. At present there are several things wrong which are obscuring each other. Being able to deal with each ne in isolation makes life much easier.
(1) Your sentence below does not make sense. Can you please explain more clearly what you mean. "The MOSFETS are connected" and "drain and source ... connected" can both mean the same thing. If they DON'T mean the same you need to explain what you mean. You said:
(2) This would be fatal:
As Oli says, presumably you mean Vdd = Vcc. You need to read what you write before sending. We all need to and we all get it wrong sometimes BUT when you are asking the questions and want help then confusing the assembled masses with typos is a very bad idea.
(3) This probably means that your IC is dead or walking wounded OR you have a disconnected line - possibly ground. When things go this wrong you need to carefully measure everything - voltages when on and ohmic connections when off. look for shorts AND opens.
(4) If you were using "real" voltages your IC and random other things would now be dead. Shorting the capacitor connects the isolated high voltage "island" in thje IC to the drain of the lower FET which gets connected to ground when the lower FET is turned on. Shorting this cap could be an extremely exciting and non productive thing to do in many situations. Hopefully you determined before you did this what you expected to happen and didn't just do it to see what happened. When you are dealing with power rather than signal the magic smoke is never too far away. You may have had some already without being aware of it.
(5) Making the capacitor 100 times larger than you calculate in a circuit that may be switching at 10's to 100's of kHz is highly likely to produce interesting results. These could include an interesting emulation of lot's wife. But may not. The capacitor has to charge in the time that the low side FET is on. It discharges when the high side FET turns on. There will be charge & discharge time constants controlled by the resistance in the IC power paths. This may still work OK OR the voltages may only rise to a fraction of what is intended in the time available. Which may be consistent with what you are seeing.
I could add a bit more but that should do to start :-). Sometimes we all have a bad day - you need to try and not let too many things at once get out of control as then you can't asily analyse what is going wrong.
As others (and I) have suggested, measure everything you can and see if it makes sense. If you have an oscilloscope see what it can tell you. If you don't have a'scope, start putting lunch money aside for one. Even a relatively cheap scope can be a mightily powerful tool. An oscilloscope is possibly the most effective and powerful debugging and fault finding aid you will ever have for analog circuits.
Practical aspects:
If hand driving at low speed, connect Hin and Lin and SD low with pull down resistors. Then, if you hand switch them and they "bounce" they will bounce from low to applied signal level and not to some unknown state.
BUT the bootstrap powering circuit for the upper gate completely relies on there being an AC signal at VS to supply AC at Vb which draws power from Vcc and delivers it to Vb. If there is no AC your =upper gate signal will decay "rapidly". How long it takes depends on upper driver power consumption and was part of your capacitor calculations (from memory). This is an example of where an oscilloscope will help you see what is happening. The 100 uF you are using is a large value and decay time may be long enough to see what is happening "by eye", but maybe not.
If you want to drive with a microcontroller you could reduce Vcc to Vdd rather than raising Vcc - as long as IC minimum voltage spec is still met.
Re-etch of PCB MAY be a good idea BUT you should be able to carefully go over circuit and check that what you have is what you intend. Do it pin by pin.Talking to yourself about it as you go can help :-) (really). Describe what you expect to see and what you really see and why they are or aren't compatible. [Watch for men in white coats observing you suspiciously when you are talking to yourself - or do it in your head or, works well, get a knowledgeable friend and explain it to them. The very act of explaining often works wonders.]
Schematic:
The absolute worst is when people get really lazy and lay out a symbol in physical pin order. Sometimes they'll try to excuse that by saying it helps in debugging. Even if you believe that, it only helps a small part of the time but obscures the circuit all the time. Most of the time in debugging you look at the schematic to see which pin to put the scope probe on, so a nice layout still works fine for that. It's very rare to know the pin you want and then look at the schematic to find its function. That's certainly not a excuse for being lazy and optimizing the schematic for the 1% case while pessimizing it for the 99% case.
Circuit:
Best Answer
Some people/places like everything to be schematic driven. That way the only changes to the design come from one guy/department. So even though you could add mounting holes in layout and connect them to a net, you put them on the schematic instead. That way you don't have to rely on a note to the layout guy to "add four holes and connect them to GND net". You may also have a bunch of predefined holes and you want to make sure that version gets into your layout.
In the case where you are not connecting the holes to any net then you might want to make a mounting hole as a mechanical part (no nets), just so when you push from schematic to layout the mounting holes automatically get pulled in. This is useful not just for board mounting holes but also for say a heat-sink that goes with an IC.
Really it's just a way not to forget about them or to make sure the right holes are associated with the part or board. You might make the decision on what holes to use well before you get into layout so why force yourself to remember. Especially when your boss is screaming at you to get it released :)