+1 on keeping the front drain hole clear- just do it every few weeks as a matter of course, part of the usual maintenance.
Just for peace of mind, check all of the mechanical parts- swingarm pivot bearings, rear wheel bearing etc- just grab the rear tyre at the back and try to move it side to side.
Cush rubbers will do this- remember that riding in the rain your riding style alters as well, you aren't as hard on the power, don't lean as far etc. So some faults show up more when you're riding gently and smoothly, and some when you're riding normally. Wheel out to check- temporarily you cn pack them out to get a snug fit with plastic sheet pieces cut to size (don't use cardboard....)
Check plug caps are properly pushed on to the plugs, and that plug/plugs haven't loosened in the heads.
Swap plugs for some old ones, or if yours are old, fit new ones, to see if that helps.
Balance carbs.
Swap one coil at a time for a known good one, to see if the coil or leads are being affected.
Clutch out*.
In that order
* only joking about the clutch....**
** unless it's the clutch centre bearing....
It's not falling off, it's an upgrade opportunity.
... Phew! Thinking about it it seems to happen all the time when the tank is almost empty. Have to bars left on the gauge that is normally when I fill up or around 100 mile mark on the odometer. I'll fill up in the morning and go for a ride and see if it reduces the happening of it. You said yours happens now and again, mine happens most of the time. But then I have the piss taken out of me by friends and family for being to picky about knocks and rattles coming from the bike lol 
