Just ran into this briefly, and haven't examined it in detail or tried to reproduce it in a minimal example.
When I was probing the input current for some neurons nengo.Probe(ens.neurons, 'input') with precompute=False, rather than getting negative numbers where it looked like I should, I got very large positive numbers (like 4294951040). I think these are negative numbers that are somehow being interpreted as uints instead of ints or something like that. Things work as expected if use use NxSDK probes (with precompute=True), so that can be a point of comparison.