That is really weird. Are you sure you are adjusting all your skills (not attributes) to the correct levels? RL recalculates attributes and level from skills (and fame/infamy only for luck). Do you have any special equipment or abilities that are boosting/draining your skills? RL will not count them against your skill advances. Also maybe the attrMax and levelMax are being adjusted... did you manually adjust them at the console, and did you do 'set aaRealisticFatigue.version to 0'? I'm starting to suspect that maybe another mod is screwing with things... or maybe you've discovered an obscure bug in RL. Can you do this for me;
I also experimented with changeing from one race, updating the stats, then changing back to the original race. My character still got booted down to level 8, with a lot of stats crippled.
1) write down all your skills, do 'set aaRealisticLeveling.sumStats to 0', let RL recalc everything, then do 'sqv aaRealisticLeveling' and write down all the base* and exp* values you can see (these are the base racial+fortify offsets and advancement experience for each attribute).
2) change your race, do ''set aaRealisticLeveling.sumStats to 0'
3) change your race back, set all your skills back to their original values, and do 1) again.
4) if any of the exp* or base* values are different, let me know via IM and we'll sort this out.
The other thing you can do is use the spreasheet, plug in all your characters skills and race/class ajustments (in the top two boxes), and see what your attributes/level/health should be. The should exactly match what you have.