it probably is the syncro gears (and maybe sleaves) in the trany. i had this problem in mine and left it for a while too. then one day the third gear syncro gear got jamed. you can rebuild this yourself or have someone do it. it's not a cheap job though. i did it myself and cost me 200 or so just for parts. but i am pritty sure thats the problem. good luck
Its not what you buy...its what you BUILD!!!
1995 YJ ,SOA with 4" procomp front 3.5" BDS rear 1" shackle rear, custom stearing, 35x12.50x15 pro-comp MTs, warn xd9000i, on-board air from A/C, dana 44 rear and 30 front with 4.56, powertrax no-spin rear, custom disks rear/trutrac front, warn front shafts, HD SYE kit, HD front and rear driveshafts, Warn 4X flairs, PIAA 520 ligts and on and on and on :)