I found this issue posted in 2011 but was never answered.
http://forums.adobe.com/message/4094168?tstart=0#4094168
I am having the exact same problem as that user: I have a lot of fonts, but I only enable about 30 fonts at a time using Font Book. However, ALL 1000+ of my fonts still appear in the pull down menu in Photoshop. This causes my system to slow down and Photoshop to crawl.
Dumping my font caches is not helping. This problem seems to happen a lot and at random times. This affects ONLY Adobe products (Photoshop, InDesign, Illustrator). All my other programs work well with Font Book.
Specs:
Photoshop CS3
Font Book ver 2.2.2
OS 10.6.8 (20" iMac) Upgrading to newer OS is NOT an option.
Dumped all AdoneFnt*.lst files and restarted.
Restarted in safe mode.
Checked all fonts for corruption (all are perfect).
Tried FontNuke.app
Nothing works.
Why won't Adobe address this issue?