they are probably those well nuts, those little rubber thingy's
yep, looks like they are. I'd drill the head off and pop 'em.
http://www.oemmotorparts.com/oem5.asp?M=Yamaha&T=XT%20R%20%20125&Y=2006&L=YA-XT-R-125-2&O=FRONT%20BODY&F=YA-XT-R-125-2_AS&L2=YA-XT-R-125-2_AS