I also tried my hand at a Slime based Mana generation setup and had issued with it working intermittently. I saw a ton of Slime while setting it up, then once I had it in a near finished state, they stopped spawning altogether. I assumed something was screwing with it, so I finished my setup and went looking for the cause. After searching for a few hours with no luck, I abandoned it as a lost cause and moved on to another project. In the middle of that other project, I noticed my Mana was flowing, and upon checking, the Slime were spawning again. As the world progressed, I noticed several droughts of production, which I ended up fixing by odds and ends production and a very large Mana battery. Never figured out why the fits and starts occurred, but there may be hope for your system after all.
If you're not certain if you built in a Slime chunk, Botania has the little slime in a bottle thing that shows you where they are.
Not totally related to your post, but has anyone tested to see if slimes generated by the TiCo islands work?