I\'m running into a problem in a Magento system where saving a large number of attributes either doesn\'t work at all, or only partially works. It appears to be a javascrip
You can try the variable max_input_vars (introduced in PHP 5.3.9), by default it's 1000 so that should be enough, but maybe your configuration uses a lower amount. But I imagine the form just doesn't get through due to the major performance issues you're experiencing.
About the option labels: do they by any change have an uploader for an attribute-image? We had the exact same problem when we installed the GoMage Advanced Navigation extension on a shop with over 300 manufacturer options (the extension uses Magento's built-in Flash-uploader).
We didn't have the extension for that feature so I disabled the uploader, but the extreme performance decrease was definitely in the 300 Flash-movies being loaded. Maybe you can try lazyloading the uploader on a per-option basis by inserting a button or link instead of the movie.
Hope this points you in the right (or exact) direction.