I wouldn't say "non-compatible", but I would say that Windows take an antagonistic stand against anything that attempts to alter anything it (Windows) considers "system" or "protected", unless it comes through Windows and Windows only... ie: UAC, User Access Control. Let's point you at some links here:
1.
[REL] Silent Hunter 4 Corruption Management System (SH4CMS) by Rockin Robbins. Download and unzip that utility and read up on how RR says to set-up your folder structure. Do NOT install SH4 into the windows Program Files (x86) folder. Windows ~will~ "protect" that folder from any changes, such as you would do with mods. Also, very important NOT to play the game before using SH4CMS, so that you get a proper backup.
2. Included in RR's utility is
MultiSH4, which will allow you to do multiple installs on SH4, so that you can have several different mods active at the same time, and not have them cross-contaminate each other with their Save folder data, which is a very real problem if you do much playing with mods. There is a version in SH4CMS, but might not be v1.5
3. Also included with RR's SH4CMS is LAA (Large Address Aware), but it might be an older version also. LAA allows older 32-bit apps to use memory addresses larger than 3.4 gig, if they're able. CapnScurvy has done what could be considered the ultimate write-up on its use and installation in
Windows10; Large Address Aware; SH4 Install. This applies actually to all versions of Windows that can run SH4, though XP would benefit the least from it, due to its being 32-bit also, and can't go above 4 gig in its own addressing. Folder names and file locations are different across all versions of Windows, so you'd have to adjust a bit for your Win7 install.
Once you get things set on your install, you won't have to worry about doing things to that degree again on any particular computer, since you'd just use SH4CMS, and have everything back hunky-dory in a matter of minutes instead of hours.