The best diagnostics may be as below:

1.Just make a simplest code (not your required actual code) that could simply communicate with your target.

2.Try it on both locations as U1 and U2 and this will let you know whether there is something wrong with the basics of your application like pcb etc.

3. You said that it works in U2 location and problem in U1 location.

4. If the PCB layout at U1 and U2 is not exactly the same then check if the crystal/ ceramic resonator and/or accompanying caps are placed improperly and are picking noise (or may be faulty).

I suspect that your micro is working ok otherwise its only the clock being disturbed at U1/problem location that is offestting your baud rate which results in bad communication with the target.

Good Luck

Babar/