Sounds like you need to amplify that signal a little. The R4 has a built in op-amp. I don't know much about using it but if you decide to I'll surely tag along and learn with you.
This thread seems to be a good start:
I think you are right. I'm fairly new at all this, so learning along the way. Going to have a look into the op-amp to boost the signal as you suggest. Thank you!
I looked at the datasheet. There opamp functionality is ... strange and complex.
It looks like it is designed to be turned on and off at significant rates, and a simple thing like "put some gain, or at least a voltage follower, in between an analog input and the ADC" is ... non-trivial to figure out 
There's an option for a software trigger that looks like you can just turn it on and leave it on.
If I'm not mistaken there is code in the core to use the OpAmp. I haven't looked through it. Yet.
I'm not sure that you do need an op-amp.
You would use an op-amp to increase the sensitivity of the circuit when the IR sensor is illuminated.
Your issue is when the sensor is obscured.
Looks like this sort of basic functionality is in a core library.
I would definitely be interested in increasing the sensitivity of the IR receiver, if possible.
You could do that by increasing the value of the 10kΩ resistor.
The same photo-current through a larger resistor develops a higher voltage.
I'd try that before thinking about using the op-amp.
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