Unusual WordPress internal load times

I have two separate WordPress installations on different hosting providers with a similar (possibly related) performance anomaly that I cannot get a handle on.

I’ve been seeing poor performance from them and have tried the W3 Total Cache plugin (although I’ve removed it to debug this problem). After a lot of attempts to determine a root cause I’ve narrow it down to a long initialization time for WordPress.

I wish my test cases were better, but I hope the degrees of magnitude still make the point.

Site 1 (runs on FatCow server): time to execute require_once(wp-config.php) 2800ms
Site 2 (runs on LunarPages server): same script loads in 300ms.
Site 1 and Site 2 have the exact same plugins enabled.
Site 1 has had the W3 caching plugin (and some other plugins) installed and removed.
(I configured site2 by hand to run this test. It started with a base load time of 185ms and that rose to 300ms by the time all of the plugins were installed and activated.)
A nearly 10X difference seems improbable but there it is.

Site 3 (at Media Temple) runs a BuddyPress site. I’ve trimmed all of the plugins I can right now and load-times for wp-config.php hover around 2-5 seconds.

Is there anything at the file system level or PHP configuration that could cause such horrible initialization times? Any other places I could look?

Thank you,

– dave