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Build Identifier: I tried Helios and the first thing I noticed was that it had no auto completion. The reason turned out to be that I used a workspace from Eclipse Gallileo and Helios lost a setting under java->Editor->Content Assist->Advanced that said "Java proposal". Whern i checked that in it worked OK again. This might be corrected for new users that will fall into the same trap as I did. Reproducible: Always
I don't think the preferences got lost but rather you did not have Mylyn installed and hence no content assist. If that's not true then please provide detailed steps to reproduce.
My guess is this is the same as my problem and maybe not Helios specific: http://blog.tremend.ro/2006/10/19/eclipse-java-autocompletion-not-working/