Electronic – Why does output voltage increase when pwm input frequency to output enable increase

Shoot-through current refers to the condition where both switches/MOSFETs on one side of the H-Bridge are on simultaneously. Under normal conditions, the H-bridge is under one of the following conditions:

If, however, both switches on one side are on simultaneously, a huge current can flow (Only 34mΩ per leg, remember?), which is usually destructive. I'm not sure why both switches would be on - Possibly an issue with gate capacitance and switching time?

The datasheet says that the PWM pin is:

Voltage controlled input pin with hysteresis, CMOS compatible. Gates of low side FETs are modulated by the PWM signal during their ON phase allowing speed control of the motor.

You might get better luck with higher voltages if you modulated the PWM such that it was centered on the ON-pulses:

Motor on:     ----    ----     --      --
S-Left-Top__/------\________/------\________  
S-Rght-Bot___/----\___________/--\__________
S-Rght-Top__________/------\________/------\
S-Left-Bot___________/----\___________/--\__  

But you'll definitely want to look very carefully at Figures 4, 5, and 6 of that datasheet.

4) You have stated that you must use LM741, but for future reference, your application calls for a voltage comparator. For example, a LM393, which is from the same era as the LM741, would not give you the same issues.

Given that you are stuck with the LM741, something like the schematic below should work for what I think is your application. And it is simpler and does not require any negative voltage.

^{simulate this circuit – Schematic created using CircuitLab}

In this way both output states allow to turn the transistor on, such as V+ = 5-1.6 and V- = 0+1.6

This quote seems to imply that you have V+, the positive supply pin, connected to 5V. But the opamp inputs can be 5V or higher, so V+ needs to be higher, like +12V.

Also, from the TI datasheet, the LM741 minimum operating voltage is +/- 10V. That means it needs 20V to operate per the datasheet. But I am going to guess that 12V is probably good enough for this.

3) The capacitors as shown does not get reversed voltage during normal operation.