Can't say I have ever notice this on my bike, are you leaning over the handle bars to see this, if so I don't think it's a good idea. Check you connection on the battery, make sure they are good and tight. Did the previous owner install running lights
http://www.vtxoa.com/forums/showthread.php?205905-1800-Ground-Fix-by-Tapper&highlight=ground+fixo Ground fix
"when the brake light pulses"Does it have a taillamp modulator installed?
i assume this is happening at idle only?