I have obviously misunderstood the problem. I now understand the one input for both instruments. However, i am unsure why the Loops are required of you only ever use Guitar OR Uke at any one time.
I would try the follow experiments
Firstly, try assigning the Guitar to Main Outs and the Uke to Monitor Out Stereo. Set both to receive master stereo as the source. Then set the Guitar Rigs to mute monitor Out (volume 0) but the Uke Rigs to send Monitor Out full volume and mute the Main outs.
If you only need mono signals then just use the main outs but set the Panorama control in Rig Menu to full Left for Guitar and full Right for Uke.
Neither of these would need the Loop at all.
Alternatively, if you need to use the Loop and it is in the last slot try changing the Series/Parallel configuration (Dly+Rev Routing in Rig Menu se page 220 of the manual.
However, it may just be that there is currently a bug. I tried and experiment yesterday with parallel path and even at a setting where there should have been no signal from the Slot A and Slot B FX there was still some bleeding through.