Sounds odd. I have had some similar issues setting up our moodle install recently and have learned that calling the cron tasks via http can slow things down quite a bit during the time they are running, leading to something similar to what you describe. I run 3 separate moodle installs on one miniserver and had all the cron jobs set to run concurrently, so now i have staggered them and changed them to command line php. See here for more tips. Are you using a php accelerator?