I think the problem might lay in the level creation itself and maybe misunderstanding about single levels, packs and tilesets.
I try to explain it from scratch to avoid talking around each others.
A
level is created by the NeoLemmix editor in a .lvl file. In the
level tilesets are used that
are stored in the NeoLemmixEditor styles folder in .dat files.
The
NeoLemmix Player can load these
.lvl files directly, but
it needs these .dat tilesets in it's styles folder as well.
If you have
a lot of levels you can
put them together in a pack using the FlexiToolkit. You have to
give it all the .lvl levels, .dat tilesets and music you used (+ optional music and logos). Then you can
save your entire configuration ("Save as") in a SYSTEM.dat file (do not rename it!). You can also load this configuration again then after closing the program.
At last it can
build an nxp file which you can name properly (+ optinal music pack)
which the NeoLemmix player can load.
All in all:
The player loads packs (.nxp) and levels (.lvl). It needs the tilesets (.dat) in a styles folder (+ optional music in the musics folder). It can save replays of levels (.nxrpl).
The editor creates levels (.lvl) using tilesets (.dat) in the styles folder (+ optional music). It can also testplay levels directly by placing a NeoLemmix player in it's folder.
The FelxiToolkit creates and loads pack configurations (SYSTEM.dat) using levels (.lvl) + tilesets (.dat) + (optional music and logos in .png). It can then build these configurations into packs (.nxp) and optional music packs which the player can load in.
Maybe join our IRC live chat #neolemmix for quicker investigation. Or give me all your loadable .lvl files and I try building a pack from scratch and I see if the levels are created wrong or if sth you did in the toolkit is fishy.
EDIT: Ok wrote this before you wrote your last message, but I think it is still worthwhile posting 
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Xmas stuff is working again! Expect the skillbar needs to be updated to the new format.
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