I still think it's daft.
The OS "thinks" it is on an IDE drive, so any OS machine level code it has that would have taken advantage of the SATA drive will be disabled. Likewise any programs you are running that have I/O routines that control the hardware directly (rather than using the OS's) may either not work or may run slower than they would have done had they been installed "seeing" the SATA drive was there.
The machine may well boot apparently correctly, but you may be missing out on the enhancements (e.g. speed) that SATA potentally gives the OS and your programs.
For the sake of a few hours spent reinstalling the programs you still use, you gain a much slicker setup with all the extraneous programs, spyware, etc you don't need cleared out and now have your software stored in contiguous and hence faster to read sectors. If your old IDE drive had bad sectors by cloning it you just build the bad sector map workarounds the old drive used into your new one unnecessarily, and if it does have errors, you clone these too.