Hi.
We always try to avoid massive clearings because of the problem you are reporting. You may consider to use transaction code F.13 to automatically clear open items in pairs instead of massive clearings, that would be my preferred solution.
Anyway, if you can't avoid the massive clearings, you may also consider transaction code FLQINFACC to directly assign any account to a liquidity item, with 'Further" flag unchecked, then the system will just assign the liquidity item without navigating through all possible combinations which is your problem.
Hope that helps.