I've had similar problems lately gathering in Vash'jir for example, lots of "could not generate path" errors for hours, didnt have this issue before new update either.
Log was too big had to compress it:
2012-07-13_00_17 6488 Log.rar
upload the .zip here next time
also, you have a LOT of plugin issues
[00:56:26:951] [Gatherbuddy2]: Approaching "Stormvine" at X="-5471.865" Y="3417.345" Z="-116.9671"
[00:56:26:951] Activity: Moving to node
[00:56:38:854] Spell_C::CastSpell(5487, 0, 0xF530A20900189FC8, 0) [66]
[00:56:38:906] Casting: Bear Form
[00:56:39:900] Activity: Loading Tile/s
[00:56:39:900] Loading Azeroth_25_42
[00:56:40:017] Could not generate path from {-5449.734, 3421.833, -116.5725} to {-5379.755, 3423.477, -116.0212} (time used: 1 milliseconds) @ FindStartPoly
you're in combat and your toon can't get the required 80 yards to the mob
you should blackspot that node / take the waypoint out if it's a constant issue