Electronic – arduino best serial communication solution

As I understand, you connect your Arduino to two different target machines and on one it works and on the other it doesn't.

So it seems there is a difference between the initialization requirements of the two machines. On this page at the very bottom there is a listing of a possible initialization sequence. Start by comparing your initialization to that one.

It will be a lot easier by using a logic analyzer. I am using the Intronix Logicport, but there are both cheaper and better ones, though not at the same time.

Tapping into an open-collector bus is a bit cumbersome because you don't see which device is talking. However, if you put in a series resistor at the end where the pullup is not, you can tell by the voltage level which device is holding down the bus. Every open-collector bus (like PS/2) needs pullup resistors, usually they are built in in the PC. You can see the different voltage levels easily on a DSO. With only a LA you have to record twice with different threshold voltages.

If this is indeed an issue of analog/digital separation there are a number of electrical strategies to overcoming it. The easiest of these is to have a separate ground plane for your analog circuitry from your digital cicuitry and join those ground planes at the common return (i.e. the power input to your board). This is called a star-ground topology. I'm not sure what you're going for with the diodes you mention in your question, but you might also consider filtering the VCC to your analog circuit through a ferrite bead and capacitor, and make sure you have adequate decoupling capacitors near all the VCC pins of your amplifiers and other analog circuits.