Ok, following receipt of your site access details the day before yesterday, and your yesterday evening's confirmation that you had a full backup before we start working, we could drill down into the issues you have been facing today and we could find a solution:
I'm reporting back these good news to the community, so that others facing same issues know what to do:
We have pinpointed it to be another occurrence of the <PHP 5.2.5-unpatched bug in PHP itself, and we have spent most of the day trying to design a workaround. We could finally find a workaround to that nasty PHP 5.2.2-unpatched bug, and have implemented it completely into CBSubs 1.1. We have also back-ported the workaround into the CBSubs 1.0.3 which is installed on your site, and the issues that you faced (sporadic huge memory consumptions as well as the execution timeout) that we could both reproduce prior to the changes, on your site, have both been solved as far as we could see.
We have implemented the workaround on your site, and the issues seem to be solved.
Please note that PHP 5.2.2 unpatched has known vulnerabilities, and that an upgrade is highly recommended. But the vulnerabilities of PHP 5.2.2 were not the issue here, neither was CB or CBSubs in cause here either, but as said it's a bug INSIDE PHP 5.2.x < 5.2.6 that was the issue.
If anyone has such a host with PHP < 5.2.6 and unpatched and doesn't have choice to do the highly recommended upgrade or change hosting, please PM me for a workaround-version of CBSubs 1.0.3.
Upcoming CBSubs 1.1 will be working around that PHP bug, so I hope we can lift the PHP 5.2.6 prerequisite.