[Silent Steel]

Firstly;
Before doing anything more drastic - just to check that the JSGME isn't corrupted please read this How to Fix Mod Soup Issue by Webster closely and follow it.
One thing to point out is that when you move your mods from the C:\Ubisoft\Silent Hunter 5\MODS folder to the desktop (or wherever on your HD you like to keep them) this means the mods ONLY, NOT the !BACKUP and !INSTLOGS folders and the 'JSGME.ini' file.

Secondly;
The specs seem to be alright but after some reading on the net I can see that there are some people getting issues caused by the GPU nvidia geforce 555m.
And - just like many mates around here in the forum you could try the d3d Antilag, if you not yet haven't, just to ease the stress on the CPU. Make sure you read the enclosed ' readme.txt.txt' file as this is NOT an ordinary mod!! In the 'antilag.cfg' (open with notepad) set it at RenderAheadLimit=2 and
FPSlimit=36. Save it to the same place and make sure you save it as a .cfg file. I say this because when you save this the default is .txt file! Choose file format 'All files' and check after saving check the file still is named 'antilag.cfg'. Nothing else.

If these issues still occur after doing this I'd say it's likely that this happens because of a corrupt install. So, my suggestion is to make a complete reinstall of SH5.

Before uninstalling;
Make a copy of your 'C:\Users\'user account's name'\Documents\SH5 folder.
This is where all saves, personal settings and game progress are stored. After the reinstall - put this copy back to the same place (in the Documents folder) and let overwrite.

After the uninstall;
1. Delete all folders in the C:\Ubisoft\Silent Hunter 5 folder! If possible make a scan with CCleaner to make sure there are no leftovers.
2. Reinstall SH5
3. Run SH5 at least once just to make sure the game gets patched to v1.2.0.
Should happen automatically but if it doesn't - run the C:\Ubisoft\Silent Hunter 5\Support\GameUpdater\gu.exe
4. Download a new JSGME
5. Put the 'jsgme_setup_v2.3.1.exe' into the 'C:\Ubisoft\Silent Hunter 5' folder and run it. During this first run the JSGME should ask you if you'd like to create a MODS folder - answer Yes.
This new MODS folder must be in the the C:\Ubisoft\Silent Hunter 5 folder like this C:\Ubisoft\Silent Hunter 5\MODS.

Ready to go.
Put your mods back into the new MODS folder and remember to check that your mods do have this structure; 'mod's name'\data. Nothing more and nothing less.
Some mods come with an 'extra' folder named 'Documentation'. These contain some info on the mod and shouldn't have any effect on the mod.
I myself always take it away before dropping a mod into the C:\Ubisoft\Silent Hunter 5\MODS folder, just to be sure.

If nothing of this helps we have to look for some other solution. Please come back and tell me what has happened.
And - when/if testing with any mods activated in the JSGME - please tell me about the load order in your mod list.