First of all: Do they work outside the debugger?
- menu Run > run without debugger.
- or compile, then find the exe, and run outside the IDE.
Also, do they run if compiled with optimization off? (level 0 / -O- )
The difference in files, might be if your desktop was an upgrade from an older version of Lazarus.
The "sources" seem to have resolved to the same real path, since replacing them worked.
About the compiler exe. Here the question is, if you have another fpc somewhere on your desktop
Menu: View > Ide Internals > About FPC
There will be (somewhere in the middle)
FPC executable:
Compiler=C:\lazarus\fpc\3.2.0\bin\x86_64-win64\fpc.exe
or similar.