We recently found a bug that may silently cause problems with many simulations. The bug causes problems in the following situation:

You create a NeuronGroup
You create a subgroup of that group
You create a Connection from that subgroup
The Connection has delays

In this case, the SpikeContainer object would be improperly initialised and many spikes may be lost. The latest development version fixes this. See ticket #33 on our trac. If you have code running on an older version and think your code might be affected, please get in contact on the briansupport@googlegroups.com list.