This could be related to the (recent) change where free SPs are now calculated on the fly based on the current race bonus SP, starting (creation) SP allowance, and level-up SPs.
If your race had its race bonus SPs changed in a rules change then you could find yourself with more or less total SP (used and free). If the race bonus SP was reduced you would have lost some free SPs when the new calculation came into effect. If you didn't have free SPs at the time, your free SP would essentially be negative and you'd 'lose' the level-up SP when you levelled up. Depending on how much the race bonus changed, you could be levelling up again and not see the free SP increase.
I bug-based it when it happened to me, but admins say its not a bug but the way the system is supposed to work now, and applies retrospectively to your character (unlike say, the Med Neb ship stats change, where the old ships kept their original stats):
If any race in future has its race bonus changed, the changes will automatically be applied to all PCs of that race.
There are other reasons, apart from race bonus SP change, why you may have more/less SPs than the calculation/rules expects : perhaps you had your race changed or you had SPs awarded in an old scenario (e.g. as reward to act like cyborg implants). Any discrepancy between what you have and what your race is now supposed to have is being cleaned up by the calculation.
At least, this is how I understand it.
There is no god but Ara... All will walk his path...
The Faithful of Ara
<--- (Warning: music link)