Reposted here to ensure its visibility...
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Just to summarise and clarify the installer checks, as it seems some people for what ever reason refuse to believe the installer is right!
Trust me though, it is. It is doing a very non-emotive, methodical check of your system. It simply reports what it finds. And with these checks it won't be wrong.
The error messages and likely causes are:
Modifications installed via JSGME were found. Please disable all mods before continuing.
You have mods installed via JSGME. Simply disable them. If your JSGME displays no mods enabled, before accusing the installer of being an idiot, check your MODS\!BACKUP folder. If there are ANY files there, IT MEANS YOU HAVE MODS ENABLED VIA JSGME!!! What it more specifically means is that you most likely deleted a mod in the past without disabling it first.
Now don't just delete the !BACKUP folder and files, because whilst this will make the installer happy, it won't make you happy in 20 minutes time when your game starts acting erradically due to conflicting files caused by the wayward mod that is still installed.
SH3 Commander files were found. Please roll back SH3 Commander before continuing.
The installer found evidence of SH3Cmdr files in your installation. Open SH3Cmdr and press the Rollback button. Again, if you have done this and the error persists, then what has most likely happened is:
a) you didn't rollback correctly at some earlier time, thus leaving SH3Cmdr files in your installation.
b) you have installed other mods that are being recognised as SH3Cmdr files (because the files are similar, same name etc). Still a problem as the installer won't fail on a clean GWX installation, so investigate this possibility too and remove ALL modifications from your game.
Key GWX files were not found. This patch must be installed over a copy of Silent Hunter III containing GWX (with or without existing hotfixes). Please ensure that the selected installation has GWX installed before continuing.
If you don't have GWX installed, you must install it first. If you do have GWX installed, then the installer found files sufficiently modified as to cause problems if GWX 1.02 was installed. Remember what changes you have made and undo them. If you use SH3Cmdr, then you should be adding your specific changes to it for then they will be removed automatically on every roll back and reapplied automatically on every run, thus when things are done right, the game after every rollback will always be pristine and "ready to be patched". Steppenwolf has this spot on a few posts back.
The most common causes for this mistake will be adjustments to Basic.cfg (renown and the like) or forgetting that you unzipped other large mods directly into your installation.
Guys, please remember that the installer is trying to HELP you and SAVE you from problems later on. If you maintain proper housekeeping, you will have NO problems installing the patch, Otherwise, well, reinstalling now is still much better than fault finding later. And watching your game CTD to the desktop after sinking that large warship I guess is not a good feeling.
At the worst you will become more vigilant with your JSGME and SH3Cmdr housekeeping.