The tool you use doesn't matter at all... for example, others use Ableton and this is just fine too. Just like it's perfectly fine to make GPL software with a commercial compiler (e.g. MS Visual Studio). In fact, I wouldn't even recommend you to switch to LMMS at the current time, if you're used to another tool. LMMS is still too new and lacks some quite important features (e.g. volume envelopes, and lots of editing tools), but is already great in the rendering/synthesis department.
What matters is that you own the copyright on the result entirely and can put it under the GPL. Alternatively, you'd have to acquire the required rights from all other copyright holders.
