I recently upgraded to mysql 4.1 through WHM. I am running php 5. After i did the easyapache update (as suggested in WHM to finalize the mysql 4.1 upgrade) apache fails. Any tips? I am pretty n00bish so please bear with me .
I fell into the same problem and after digging a lot I found that you will have to run the command chmod 755 /usr/bin/flex before running easyapache something changes its permissions and this causes all the problems. I hope this solves your problem as well.