Ok so here is what I know. Apparently Z4R3 is compatible with 2048px alphas. Which a lot of the brushes are using.
So far this has worked 100% of the time from what people have told me. Upgrade to R3, if that doesn't work. Uninstall and upgrade again.
Another issue. The lag issue. I might at some point... Downres all of the alphas to 512 so they are backwards compat with all versions of Zbrush back to 3. This will take a lot of time to do, b/c I have to downsample each alpha, reimport and resave each brush. Then reupload to the site and repackage etc etc. I have tested it and I believe it fixes the lag issue as well as the back-compat issue.
If I do this I will package all of my alphas in 2048 to give away in a separate package.
I am going to do some more testing before I go through all of this trouble. So if anyone else could test upgrading to R3 if you are having alpha issues and post. This would help me very much. Remember I am doing this for the good of the community. I expect nothing in return. So a little help would go a long way