You did not attach the save. I would have thought increasing MissionNum would have done it (Mission = Mission_05 & MissionNum = 15).

JFLP is a patch to fix some things (in particular, it provides widescreen support); it also replaces the original binary-encoded *.ini files with their text equivalents, for easy editing.

The mission files are stored in folder DATA\MISSIONS where you installed Freelancer. The individual missions are in individual directories, e.g. M13\m13.ini.

Using a text editor (Notepad will do in a pinch, but you might like something with a bit more oomph - Notepad++ seems pretty popular) you can edit those files, searching for SetRep (more specifically Act_SetRep). This is the command that changes your reputation with a faction. If you place a semicolon in front of the line (;Act_SetRep ...) it will comment that line out, thus leaving your reputation with that faction unchanged.

Then it's a matter of determining which factions in which missions you want to preserve/comment.

Here's a factions list, relating the nicknames to the name.

It supplies an original exe (with a modified version resource) which no longer works. Restore your own exe and all should be good. You could replace the exe within the mod itself: open its exe directory and replace the exe with the one from no-cd exe 175 - german.

Armor offset is at 139AF8 (same bytes as cloak). The only other two options are:

50D426 - MineDropper
D0DE26 - CargoPod

and I doubt CargoPod would work. ShieldGenerator won't work (without a plugin), that needs data that Armor doesn't have (the type of shield).

I'll look into it, hopefully within a week. Strange it took so long to discover.

Could you post the mod's server.dll?

Yeah, that would do it.

As for your crash, could it be an intro? Nothing in the spew?

I just remembered they're not all "Navy" after all:

li_n_grp Liberty Navy
br_n_grp Bretonia Armed Forces
ku_n_grp Kusari Naval Forces
rh_n_grp Rheinland Military

I guess that makes them more or less a straight translation:

Marine - Navy
Streitkräfte - Forces (according to Google Translate)
Marinestreitkräfte - Naval Forces
Rheinwehr - Rheinland Military (no, I suspect that's something else)