Don't know if anyone has found a fix for this or not, but I've noticed this as well. Seems to be really impacted if you are using Media Manager. I am on hold with BB tech support to see if they can come up with a workaround.
AT&T Desktop Manager 4.6 (460_b016_multilanguage.exe)
Windows XP PRO SP3 part of a domain
2 to 3 min. delay at Applying Computer Settings or Applying Personal Settings. Not sure if this is because of the way GPO's are being applied. (ascyn or sync)