Instrumentation of files not in main folder seems to not occur

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Have a project that use .pas files in other folders. The type you must check 
"Show all Folders" option in Instrumentation page.
2. Instrument it.
3. See that the files are not changed

What is the expected output? What do you see instead?
Expecting the files are prepared for instrumentation.
The files in these folders are not changed at all.

What version of the product are you using? On what operating system?
1.3.5 in Windows XP

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 31 Dec 2011 at 1:50

[GoogleCodeExporter]

I've discovered that this was not what seems. The problem is that the program 
was changing files for other compiler version. Probably, using a different 
search path from what was configured.

Original comment by [email protected] on 8 May 2012 at 8:19