Every version of FLMM has had some variations in the XML scripting, this wasn't a problem as long as you added the "scriptversion" TAG to the xml file, this way FLMM knew which xml version to use. IGx89 changed the xml script for 1.4 but he also "fixed" part of 1.3's scripting, this means that any mod that works fine with FLMM 1.3 might give an error message with 1.4 (CrossFire for one).
I was one of the people that tested 1.4 when IGx89 first released it (thats why theres four versions of it) and it was only after I lost 4 Gb of harddrive space that I found the other problem with 1.4. The new "cache" feature screws up the deactivation of a 1.3 or older mod, rather than deleting the mods custom files it leaves them behind in the Freelancer folder, all custom system, base & room ini's, CMP, 3db, MAT, SUR and thier folders are left untouched by 1.4. With FLMM 1.3 I very rarely had to do an uninstall/reinstall of Freelancer but with 1.4 I had to do it every time I used it, I only have a 20Gb hardrive so I can't afford to lose the space.
IGx89 knows about these problems as there are threads in the FLMM forum here on TLR about them, I've also emailed him my findings but as it's been more or less 6 months and I/we haven't heard from him, I've started to wonder if he's even interested any more.
**shuffles of with a new headache**