My guess is it's an issue with the eaccelerator loader. I've found the majority of the time the build matching php binary it'll be unable to load the modules built by easy apache. The error that is probably being produced is about matching symbols on the eaccelerator module (I think that's the error). You will not see the error on pages as it's a suppressed one although it might appear in the error_log if php is writing one to folder the php script ran from.
What I've done is when I build the matching php the first time I also take the modules folder files (pdo, pdo_mysql ect.) and put those into the php extension folder. I also then grab the cli files built and overwrite the existing ones. Then things like eaccelerator I can build manually. Then the lsphp and cli php are both compatible with each other no errors on either end.
I have absolutely no idea why this happens but this is my experience with that. A few cases it did work fine other cases it did not and I have no idea why.