atapi error

hi,

i seem to be having a problem with my system,
if i switch my system on after a long 'off' period (eg overnight) and boot into windows it takes about half an hour before it becomes usable,
this log is in my application logs, duplicated many times

Event Type: Error
Event Source: atapi
Event Category: None
Event ID: 9
Date: 11/02/2008
Time: 12:39:03
User: N/A
Computer: (took out)
Description:
The device, \Device\Ide\IdePort0, did not respond within the timeout period.

if i boot into linux, it takes about 30 secs - but if i then switch to windows, its usable in about 2 mins with no error logs.

if i allow it to first boot into windows fully and then re-boot into windows, it only takes about 2 mins for the second boot with no error logs for the second boot,

anyone any ideas ?

grub bootloader controling

linux = master hdd
w2k pro sp4 = slave hdd

checkdisk = nothing
full virus + malware scans = nothing
more info = just ask

ta