I'm pretty sure I've found the culrprit, I'll type out an explanation here for you to give to your host:
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I believe that the issue lies with the suhousin module installed on the server. By default suhousin will limit the amount of variables that php can read as a protection from buffer overflows. With our script, UBB.Threads, when the config file (config.inc.php) is written it will submit all configuration variables as post data which can exceed the amount of variables which suhousin can process; this limit will need to either be removed or increased to alleviate the issue where the config file will write blank data which will disable the forum until a backup file can be restored.

And I'll type out a statement for the search feature so that this thread can be easily located in the future:
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Too many configuration variables are being submitted for the "suhosin" module and it's clearing out the configuration "config.inc.php" file.

I really just want to quote Rick, who is missed dearly
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suhosin strikes again. For anyone following along or comes across this in a search. suhosin is limiting the amount of form variables that can be passed to the script and discarding the rest.

More information on what "suhousin" is, that I posted in one of the threads I'm linking to below:
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Suhosin is an advanced protection system for PHP installations. It was designed to protect servers and users from known and unknown flaws in PHP applications and the PHP core. Suhosin comes in two independent parts, that can be used separately or in combination. The first part is a small patch against the PHP core, that implements a few low-level protections against bufferoverflows or format string vulnerabilities and the second part is a powerful PHP extension that implements all the other protections.

Unlike the PHP Hardening-Patch Suhosin is binary compatible to normal PHP installation, which means it is compatible to 3rd party binary extension like ZendOptimizer.

Here I will provide some "handy dandy" references so that I don't have to hit my head against the wall next time:
Display and Feature settings gone and will not reset
7.5.5 all moderator permissions gone if you try to update mod group
Losing forums??
Losing forums??

In fact, you might as well just link your host to this particular posting, with this url.

Go figure I get free time in the half an hour I wake up to my morning coffee while getting my son ready for school, lol.

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