Dear Dkaneloglou,
There is a VM-imposed limit of ~19.000 characters of configuration data for each shipping method. The issue is that the database that VM uses to store the method's configuration data has allocated a field of that size for the configuration data. If a shipping method tries to save a configuration (in this case rule sets) of larger size, the database will simply refuse to save it at all, effectively clearing all fields.
As this is a core VM issue, there is nothing that you can do in the shipping plugin (the shipping method configuration page and the settings loading is handled by VirtueMart, not by the plugin!).
However, as Eliot already noticed, one can try to split the rulesets into multiple sets and use multiple shipping methods for them.
As you correctly notice, though, one has to take care that only one of the sets matches. In particular, fall-through / catch-all rules are very problematic in these circumstances, as one shipping method has no way of finding out whether another shipping method already offers a rate.
One typical factor to assure mutual exclusive rules is the countries setting (e.g. use one method for each country set).
The other approach to the issue is to try to minimize the size of the ruleset by combining multiple similar conditions into one method.
Best regards,
Reinhold
