What version of Yosemite?
When you say "updates", what version of AE are you using?
I've not heard of anybody else with this problem, so it's likely to be something fairly obscure. What third-party plugins do you have installed?
I use OS X 10.10.3. I've just installed the after effect CC 2015, and each time my apple keyboard have some difficulties to work. It appear only in after effect CC 2015.
I have lot of third party plugins:
Row Bytes plexus and data glitch
MB resizer and instant HD
RE: vision plugins
All work very well with CC 2014.
All of your plugins need an updated version to work with CC 2015 (that's unlikely to be your issue, but old versions of plugins have been causing all kinds of issues with CC 2015 lately so...).
Same problem here. Keyboard input lags strangely - when renaming compositions, using shortcuts, typing anything really.
Windows 8.1 64bit
AE CC 2015.0 - 220.127.116.117
Same here. No Plugins installed. Just Standard AE. Sometimes it's fine, others I can't get a keystroke to work for minutes at a time.
Well, unless you enjoy being an unpaid Beta Tester for Adobe, I recommend sticking with AE CC 2014 until the many bugs in the newest version get sorted out.
Which means if you weren't careful when you installed CC 2015, your older versions aren't there anymore. Which means you have to reinstall the old versions.