Can IR emitter signal be distorted by curved glass housing around receiver?
Short answer: No.

Long answer: you can of course create shadowing that way, and that would disturb operation. And of course, a glass wall will refract infrared just as it refracts any other light. But glass is usually IR-transparent, just as it is transparent visible light, and an IR remote isn't exactly a source of a focused beam, so chances are that, no, there's no difference in operation.

What will happen is that the IR will be a tiny bit weaker, due to absorption in the glass. But that won't be really much, I guess. 


  Could the jam jar's reflection and refraction be impacting the length of the pulses? 


How so? It's the same signal entering and exiting the glass. Admittedly, at a different position, maybe a bit attenuated, but still, if you wanted to change the duration of the pulses, then you'd need a frequency converter (which is a nonlinear device) or a time machine. You have neither.

What could be happening is that due to reflections in the glass, at the receiver, you'd get one received signal that took "the shortest" path, overlaying with a "delayed" path. For that to have any negative effect, the path length difference would need to be in the order of the duration of your pulses.

Infrared remotes work with longer pulses modulated to something like 38 kHz, if I remember correctly. Ignoring that wavelengths are different in glass (factor of maybe 1.5, and we're just here to get a feeling for the orders of magnitudes involved): a signal travelling a speed of light travels, in one period of a 38 kHz signal, 
$$\frac{3\cdot 10^8\frac{\text m}{\text s}}{3.8\cdot 10^4\,\text{Hz}} \approx 0.7 \cdot 10^4\,\text m = 7\,\text{km}$$

Since any distance your "detouring" beam might take will be way, way smaller than that, we can rule that out.

I think for the typical roughness of a marmelade jar glass, we can also rule out thin-film effects on the surface.