@Gioronco: to give a proper (and useful) report, please say us what HFS are you using, and your complete system/hardware specs, like:
1) What is your operating system, installed RAM and CPU model?
2) Are you using the default HFS's template or applying some .diff.tpl and .events file?
3) Which is fastest on your system: HFS v2.3m or HFS v2.4.0 RC7? (always make a backup of your *.ini, *.vfs and *.tpl files before doing any test).
900 folders seems to be a low amount of folders to give performance issues (perhaps the problem are your 100 accounts, and the permission rules you applied to them). Your answers are important to know if the problem was recently introduced or not (to know if there was some "regression" on the latest version).