Download the latest beta of FLMM v1.2 here: http://lancersreactor.com/t/forum/topic.asp?Topic_ID=17427&Forum_ID=18, and if that still doesn't fix it, send me that ini file so that I can take a look at it.

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Freelancer Mod Manager: newbies' dreams come true
Belief in Jesus: the only way to Heaven

Well... it fixed almost all of the MODs.....
except the Jedi Star Fighter MOD
and some error with other MODs saying something about

cannot find file "C:\Program Files\Microsoft Games\Freelancer\EXE\flmm*.dll

" * " I found it a number from 1-9 for every MOD that loaded successfully but says it doesn't find that file... @_@

and still the error of Jedi Starfighter....

Error: problem activating 'Jedi StarFighter' on test run
Error: Unable to find a section in 'C:\Program Files\Microsoft Games\Freelancer\data\equipment\market_ships.ini'

oh well here are some bugs to fixed until the release of... FLMMv1.2

Are you ready to meet your maker?.... Oh well... Whatever...

If the errors keep coming, download the Freelancer original INI's from the downloads section, and then replace the ones that don't work - worked for me.