OK, so I downloaded the WPMU 2.7 and 2.8.6 zip installs from Trac and have gone through the manual upgrade of WPMU from 2.6.3 > 2.7 and then 2.7 > 2.8.6. Yes I know there's 2.9-something out now, but I'm a late-adopter :-)
Anyway, after both upgrades, it stuffed up the file permissions in wp-admin, wp-includes, the two files that get replaced in wp-content as well as all the WP files at the root level too (it set all files to -rw-------). It left the directories untouched though - just the files.
I've done plenty of manual upgrades before (right from 1.5 upwards) and I've never had any such problems. I was wondering if there was a problem with the zip files from Trac or if it was just me (probably the latter!)?
Any ideas or has anyone else experienced this?