Resolved Sporadic Slow Operations

Hello All,

I am trouble shooting the following system:
Home Built XP Pro SP3 all updateds installed, EQS Motherboard P4 3.2Ghz, 2GB of ram, ATI 128MB on board graphics, memorex CD rom drive, 1.44MB floppy disk, 1 system hdd 60GB, 1 backup 30GB hdd.

My Problem:
When powered on it can take approx 5mins to boot. When logged on and I try to open windows explorer it takes about 3-5 mins to open and its much the same for all tasks after that.

Things I have tried:
updated my anti-virus softwear disconnected from internet and run full scans on both drives-twice....they appear to be clean.
run registry mechanic...problem still there.
booted into safe mode problem still exists.
all tempatures in bios are well within limits.
used msconfig and selected diagnostic startup problem still exists.
device manager looks good and reports no problems.
run chkdsk /r and it took about 6 hours to check and repair.

Notes:
task manager is the only app that works normally, I can access all features with it in normal time!!
the primary hdd has s.m.a.r.t. enabled (auto) by default in the bios as does secondary hdd.
when slow boot happens I notice that the secondary hdd status is echo'ed to screen as "no"
when it boots normally its set to enabled.

as I say this is spordic but the common factor seems to be s.m.a.r.t.

any ideas????

thanks in advance.

 

Thanks Pete, secondary was set to PIO...I selected DMA if available and rebooted (and turned computer off) a few times and DMA stays selected.