My first step when fixing someones PC is usually to run CCleaner and I have to say I also have noticed that it seems to have a big effect on some PC's (speeding them up) and none on others.
I never really thought much about why till I read this, and the only reason I can think of is the IE favorites are all lots seperate small files rather than one database file like some other browsers. Lots of small files take a lot longer to process than one big file. So this would be AV scans, defrags, indexing, or caching or backup, Sync of any sort. Theres also the possiblity that these are corrupt in some way which might cause problems with processes like the above in reading them. So by clearing them you speed up these processes.
That my guess anyway.