Auto-updater requires misses a file, requires second round to finish job

I updated three live boards from 3.0.8 to 3.0.9 yesterday . Each has a fair number of mods but the code of each is the same as that in the others. Each time, I found that I had to run the auto-updater an extra time to pick up changes to includes/function.php. More specifically, here's what happened for each forum:

• In the first round, after the updater checked the files, it listed lots of 'yellow light' files where it needed to merge changes but it listed only one 'red light' file where I needed to resolve some conflicts.

• The 'red light' file was styles/prosilver/themes/colours.css. I told it to merge the changes and, in the conflict blocks,, preserve the existing code. I figured that when it was done I would go into that file and fix those conflict blocks by hand.

• I downloaded the changed files via zip format, uploaded that zip file to the root of the forum via ftp (using filezilla), expanded the zip and clicked to continue the update.

• The updater checked the files again and then - rather than finding all files up to date - it reported that includes/functions.php still needed to be updated and gave me the option to merge changes (it was listed as a 'yellow light' file with no conflicts).

• I selected the option to merge changes, downloaded the changed files via zip format, expanded the zip locally, uploaded that single file to the includes folder and clicked to continue the update process.

• At this point all went well (the updater checked the files again and reported that all were up to date and the update went perfectly after that).

Not sure why this happened, but I note that the same thing happened to me when I updated these forums from 3.0.7-PL1 to 3.0.8 (although if I recall properly I had problems with more than one file and not just includes/functions.php).

I did check permissions on the site (I had a thought that perhaps the permissions for includes/functions.php were set differently than for other files in the includes folder) but they seemed fine (644 for functions.php and for other files).

Unfortunat3ely, in my haste to get the live sites updated, I did not save the original update_3.0.8_3.0.9 zip (it got overwritten when I ran the updater that second time for each forum) so I can't tell whether there was something odd about the supposedly merged functions.php file in that zip (or even whether that file existed in that zip). I also neglected to check the list of files that got expanded when I expanded the first update_3.0.8_3.0.9 zip file at the root of my forum so I don't know if something odd happened on expansion (but the fact that it happened for each of my three forums struck me as suggesting it was something more basic than an intermittent glitch in my host's expand feature).

Anyone else seen something like this during the update process?