I think this is also relevant to an earlier thread:
http://groups.google.co.in/group/microsoft.public.windowsxp.general/msg/2b0d8cc479692830
"CHKDSK is hanging on stage 2 of 3 (verifying indexes)". (The
"solution" suggested was to run chkdsk with the parameter /I, but I
will not enter here into a discussion on the merits of the solution.)
I have been having the same problem of chkdsk becoming very slow to
start "verifying indexes". This happens when I run chkdsk inside
Windows, without the /F parameter, and also chkdsk at boot-up.
The reason for addressing this reply to John is that my problem
(chkdsk slowing down at Stage 2) started after I installed Zone Alarm
(ZA). It may be a case of "post hoc ergo propter hoc", but Chkdsk
"deleted" a file C:\WINDOWS\Internet Logs\backup.rdb, which, I learnt
later, is created by ZA. Curiously, I found that this file cannot be
deleted manually in normal Windows mode, even after shutting down ZA
-- it can be deleted only in safe mode. How does chkdsk "delete" it,
if at all it does so?