I believe I have identified the problem with your processes running so long. It is waiting on a read statement:
read(3, "\7\0\0\1\0\0\0\"\0\0\0", 16384) = 11
This would seem to be the culprit that is causing your index.php to take so long to complete. The following strace output shows what is occurring right before the above:
poll([{fd=4, events=POLLIN|POLLPRI}], 1, 0) = 0 (Timeout)
write(4, "B\0\0\0\3DELETE FROM wp_statpress WHERE date < '20091017' AND spider <> ''", 70) = 70
read(4, "\7\0\0\1\0\0\0\"\0\0\0", 16384) = 11
time(NULL) = 1258432578
poll([{fd=4, events=POLLIN|POLLPRI}], 1, 0) = 0 (Timeout)
write(4, "1\0\0\0\3DELETE FROM wp_statpress WHERE date < '20091017'", 53) = 53
It seems wp_statpress is what is causing the problem.