Ubercart

Okay so I've managed to track the problem down a bit:

1. When there are only a few attributes and options, the "uc_object_options_form_validate" and "uc_object_options_form_submit" methods both get called and they run and finish (They reside in the "us_attribute.admin.inc" file).
2. When there are many more attributes and options, the mentioned methods won't get called, thus won't run.

(I've tested it with PHP's die() function.)

Could it be a Drupal bug then?

Further digging into the problem, I've tried a new drupal instance on my server at home, which runs windows. Everything was up to date: Drupal, Ubercart, related modules; and was exactly the same as on the main server which runs linux.
The bottom line: this problem didn't occur on my server, everything worked exactly as it should. This rolls the problem over to the apache / php installation on the server which I'm using.
Nevertheless, if I may suggest, the ubercart's option management page should be split into separate parts, the parts should be all subpages where only one attribute's options can be managed.
I'm trying to contact my server provider for further assistance, and will post the resolution for this problem if it will be cleared.

I've managed to solve this problem. Turns out this wasn't ubercart's, nor drupal's fault. The problem was with a PHP extension named Suhoshin. This is a security extension which limits certain POST and REQUEST messages.
In order to overcome this, you need to create an unmodified php.ini (the default php.ini which you currently use) file in your drupal root directory, and add the following lines below everything:

suhosin.request.max_array_depth=4096
suhosin.request.max_array_index_length=2048
suhosin.request.max_name_length=2048
suhosin.request.max_value_length=650000
suhosin.request.max_vars=4096
suhosin.post.max_array_depth=8048
suhosin.post.max_array_index_length=1024
suhosin.post.max_name_length=2048
suhosin.post.max_totalname_length=8048
suhosin.post.max_vars=4096

If the problem still occurs, just increase these values.