Is the console showing no rain (i.e. 0.0), or no signal (i.e. —).
I don’t believe that this is a WD issue. If the base missed the event, then with your arrangement (i.e. WMR100 feeding data to WD) WD will inevitably miss it too.
I also have an RFXCOM Receiver. The RFXCOM has much more reliable reception than my WMR200 console. It seems most likely that your problem is with reception of the rain gauge by the console. Again referring to WMR200, I find that reception of the rain gauge by the console is the one most likely to occasionally fail (perhaps because the rain gauge is low down?). In my case that is not a problem, since it is RFXCOM collected data that I feed to WD (via Meteohub[1]).
Perhaps you need to consider repositioning either your rain gauge or the WMR100 console?
[1] How do I setup WD and Meteohub to work together? - Updated February 11th 2009.