If there is a UserRoot set in miktexstartup.ini (e.g. by adding one in the Settings Dialog), there are problems with portable MikTeX.
E.g. Update-Wizzard seems to treat the UserRoot as if it was the main root and wants to download the whole distribution again, into the UserRoot. Which renders Update-Wizard unusable until you remove the UserRoot manually.
2009-07-09 21:01:24 UTC in MiKTeX