You answered your question, you are running it in safe mode. Safe mode has default settings and will always return to those settings every time you boot the computer up. Safe mode was designed for doing repairs on the operating system and not designed to be run as the main operating system, it is also limited in what it can and can not do. Basically it uses generic drivers.

OK, i just noticed you mentioned not being shut down properly, so you want an answer to get it back to booting normal. If you have the Windows CD boot it up and choose r for repair. Then choose 1 when it ask what windows, then type: fixmbr, press enter, answer yes, next screen type: fixboot, press enter, answer yes, next screen type: exit and remove the CD before it boots back up. This only fixes the boot sector of the hard drive. Some time this will get the computer to boot back into the Windows the normal way. This may not be the answer but it is a starting point.

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