I run + cycle, so I'll throw out my two cents -- and I don't claim to be an expert. First, though, what's your running/cycling schedule like for a typical week?
If you're losing speed, then you need to start training for speed (which means you'll need to decrease your endurance training to compensate). So replacing one or two of your long distance runs with shorter, but faster, interval runs may get you back to the pace you want.
The only time cycling AND running has ever hurt my form (for either sport) was when over-training. You have to be deliberate in scheduling adequate recovery time when you're doing multiple disciplines.