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RESOLVED: I posted this same thread on JustLinux's forums, and it was suggested that I try WineSetupTK. I did, and it took care of my registry files for me...so if you're having the same problem, I highly recommend it! If you don't like the generated config, just back up the one you had and don't use it. At least it fixes the registry.
To someone who knows the answer, this is a simple question, but to me...well I'm starting to get pissed at the Wine documentation. When I run winecheck, I get the following:
This script verifies the configuration of the whole Wine environment.
Note that this is an ALPHA version, and thus it doesn't catch all problems !
The results of the checks are printed on the right side:
OK - test passed without problems.
NOTICE - Not a problem but something for the user to be aware of.
SUSPICIOUS - potentially problematic. You might want to look into that.
BAD - This is a problem, and it leads to configuration score penalty.
CRITICAL - A critical problem which can easily lead to malfunction.
FAILED - This problem leads to Wine failure almost certainly.
The result will be printed as a percentage score indicating config completeness.
------------------------- checking miscellaneous stuff -------------------------
001. Checking for root user... OK.
--------------------------- checking Wine base files ---------------------------
002. Checking for file "wine"... OK.
003. Checking for correct .so lib config (please wait)... OK.
>>> Checking drive A settings:
005. Checking Path option... OK.
006. Checking Type option... OK.
007. Checking device /dev/fd0... OK.
008. Checking Filesystem option... OK.
>>> Checking drive C settings:
009. Checking Path option... OK.
010. Checking Type option... OK.
011. Checking Filesystem option... OK.
>>> Checking drive D settings:
012. Checking Path option... OK.
013. Checking Type option... OK.
014. Checking device /dev/scd0... OK.
015. Checking Filesystem option... OK.
>>> Checking drive E settings:
016. Checking Path option... OK.
017. Checking Type option... OK.
018. Checking device /dev/hdd... OK.
019. Checking Filesystem option... OK.
>>> Checking drive F settings:
020. Checking Path option... OK.
021. Checking Type option... OK.
022. Checking Filesystem option... OK.
--------------------- checking system devices used by Wine ---------------------
023. Checking sound device /dev/dsp... OK.
024. Checking audio mixer device /dev/mixer... OK.
025. Checking MIDI sequencer device /dev/sequencer... OK.
----------------------- checking registry configuration ------------------------
026. Checking availability of winedefault.reg entries... CRITICAL (entry "SHAREDMEMLOCATION" not found in system.reg registry file).
- ADVICE: file winedefault.reg, the most basic wine registry environment, doesn't seem to have been applied using regedit.
027. Checking availability of windows registry entries... NOTICE (entry "Default Taskbar" not found).
- ADVICE: A Windows registry does not seem to have been added to Wine as this typical Windows registry entry does not exist in Wine's registry. A complete original Windows registry entry set will *not* be available with a no-windows install. Usually this will present no problem in running applications although this can affect newer programs. Feel free to ignore this message in case you do use a Windows registry, but have the SaveOnlyUpdatedKeys config setting set to N..