You are doing complex calculations inside an Interrupt Service Routine. This is not a good idea. Computing sines takes a large amount of time as this consists of multiple, complex floating point operations. Interrupt Service Routines should be short and as simple as possible.

This is probably the reason you can't have two PWM signals active at the same time at the same frequency. The ISRs simply take too long.

The solution would be to pre-calculate the desired waveforms or greatly simplify the waveform calculations (preferably without floating point). If you decide to pre-calculate, take care to stay within the limited amount of memory you have available on your Arduino.

This leaves the conversion of your PWM output to a real sine wave. How are you planning to do that?

You are doing complex calculations inside an Interrupt Service Routine. This is not a good idea. Computing sines takes a large amount of time as this consists of multiple, complex floating point operations. Interrupt Service Routines should be short and as simple as possible.

This is probably the reason you can't have two PWM signals active at the same time at the same frequency. The ISRs simply take too long.

The solution would be to pre-calculate the desired waveforms or greatly simplify the waveform calculations (preferably without floating point). If you decide to pre-calculate, take care to stay within the limited amount of memory you have available on your Arduino. You can minimize the memory used by calculating and storing just 1/4 of a complete waveform and constructing the remaining 3/4 from these values.

This leaves the conversion of your PWM output to a real sine wave. How are you planning to do that?