If you've used a true dual headed IR emitter, like the one I linked, then you should play with the extra box. If not, you may still want to pick one up and give it a try.
The 3.5mm splitter listed above won't work as that's a stereo unit and IR emitters are mono.
I've certainly just put two emitters together with good results, but I've also had the same issue you have had. It makes a significant difference to use the two headed emitter because it's actually designed to work properly out of the box. Cheap emitters have LED diodes which can suck power incorrectly. Xantech dual headed models are the gold standard in the industry (for a reason). Yes, I've probably used half a dozen different brands, I always go back to Xantech, and if you ask around, it is often Xantech which is recommended.
Of course, you can just swap your IR kit out with a Xantech unit if nothing ends up working for you.