The latter, so my command was not the correct one, I guess. But if I execute the first command I get:

/usr/sh: TruecryptGUI: not found

while ls of the directory gives:

TruecryptGUI

so the file is there...

It could be missing some required libraries - what does "ldd /usr/bin/truecryptgui/TruecryptGUI" give?

libQtDBus.so.4 => /usr/lib/libQtDBus.so.4 (0x40025000)
libQtXml.so.4 => /usr/lib/libQtXml.so.4 (0x400c8000)
libQtGui.so.4 => /usr/lib/libQtGui.so.4 (0x40120000)
libQtCore.so.4 => /usr/lib/libQtCore.so.4 (0x40c3e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x40f37000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x40f57000)
libm.so.6 => /lib/libm.so.6 (0x41038000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x410ae000)
libc.so.6 => /lib/libc.so.6 (0x410c0000)
libgthread-2.0.so.0 => /usr/lib/libgthread-2.0.so.0 (0x411e5000)
librt.so.1 => /lib/librt.so.1 (0x411f1000)
libglib-2.0.so.0 => /usr/lib/libglib-2.0.so.0 (0x41200000)
libpng12.so.0 => /usr/lib/libpng12.so.0 (0x412dc000)
libz.so.1 => /usr/lib/libz.so.1 (0x41304000)
libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x4131c000)
libgobject-2.0.so.0 => /usr/lib/libgobject-2.0.so.0 (0x4138f000)
libEGL.so => /usr/lib/libEGL.so (0x413d0000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x413da000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x413e9000)
libXrender.so.1 => /usr/lib/libXrender.so.1 (0x41407000)
libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x41417000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x41440000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x41457000)
libdl.so.2 => /lib/libdl.so.2 (0x41546000)
/lib/ld-linux.so.3 (0x40000000)
libIMGegl.so => /usr/lib/libIMGegl.so (0x41551000)
libexpat.so.1 => /usr/lib/libexpat.so.1 (0x41565000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x4158b000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x41595000)
libsrv_um.so => /usr/lib/libsrv_um.so (0x415a1000)

That all looks okay anyway. The only other things I can think of to check are "file /usr/bin/truecryptgui/TruecryptGUI" to make sure that it's compiled for the correct architecture (though I think ldd would have complained about that anyway), and installing strace and running "strace /usr/bin/truecryptgui/TruecryptGUI" to check where it's actually getting the error.

This is really annoying. Now i am in the correct directory, and when i do 'ls' it returns "TruecryptGUI", however, when i then try to run this program or try to get any information about it xterm says it doens't exist... How's that possible?

Without permission the User might not be able to see it while Root may. The strange thing for you is that Root are not able to run it either. Have you tried to Chown it to User? Although that is most likely not it.

Have You done some ftp transfer?

I just tried chowning it to user, doensn't have any effect. I can access file permissions trough "ls -l TruecryptGUI", but when i try for example "file TruecryptGUI" it says that the file cannot be found.

@m750
I have transferred the .deb file via FTP. Other than that I haven't used FTP for anything.

verify that the transfer is in BINARY mode

No effect... I have transferred the deb file through mass storage mode, but still the same effect. I seems like TruecryptGUI isn't recognized as a program or something...

edit:
I just checked if I can still run the program straight from QT without packaging, however, I get the error:

chmod: /usr/local/bin/truecryptgui: No such file or directory

Maybe it has something to do with the errors after packaging? Only I have no idea why it tries to chmod a directory /usr/local/bin, because that doesn't even exist...