Odd. I've used blackra1n plenty, and have yet to encounter anything close to what you describe...
Have you ever had the phone jailbroken before by any other means, and is it possible that you had restored from an iTunes backup of your phone when it was jailbroken? I'm wondering if the installed applications cache and/or Springboard's plist (which contains the order and visibility status of icons) was in a funny state from a prior jailbreaking, and there was a strange interaction between the Cydia install and some old, stale configuration/plists from a prior backup.
You should be able to clear out any hidden icon settings by turning on Restrictions in Settings, hiding some random icons, and then turning Restrictions back off. See if your icons appear after that if this happens again. Or, install SBSettings and go into Hide Icons ("Poof") and see if any are set to "On" by any chance.
Another thing you can try is to install Erica Utilities through Cydia and then, as the user 'mobile' and NOT 'root' (which is kind of counterintuitive at first glance...), run 'uicache' from a terminal (ssh'd or with MobileTerminal), which will cause Springboard to rebuild its application cache. If they don't show up after that without any other action needed on your part, then respring or reboot.
-- Nathan