Random MySQL/Apache shutdowns - please help!

Guys, I'm getting pretty pissed here.

I'm currently working ALL DAY on a complex project with PHP.
I converted an Access database using exportSQL and I now have it on my MySQL server, which gave a huge performance boost.

Now, as I'm working for 2 hours, testing and testing, I ALWAYS get "Database not ready" error after quite a while.
Then, I have to shutdown mySQL (sometimes even Apache), then restart everything again. It's a PAIN, and I couldn't post it in an appropriate forum, because I still don't know the culprit yet.

WHAT IS THIS?

MySQL server didn't output any error message or the like, nor did Apache.

Data:

Win98 SE 4.10.2222 A
MySQL 3.23.56 started manually \mysql\bin\mysqld --console (thus _not_ as service)
PHP 4.3.1, module loaded by DLL into Apache 1.3.27

Problem:
After multiple ( > 25) tests of my PHP script (one and the same), I get 'Database not ready' error.
Sometimes, after a while, apache get's responsive again (URL works again), sometimes I even have to shutdown both.

Help, please.
-sm-