This is a classic issue; the main problem being, people keep replacing the fuse boxes and alternators but NEVER actually addressing the primary problem, which can be a bad charge wire.
Check out this video; that discusses the problem and shows how to test things and make your OWN new charge wire, that elminates the bad charge wire, which can have resistance and produce heat, melting wires and fuse boxes.
As for fuse boxes; a number of aftermarket companies, have made new and improved fuse boxes, that seem to be more durable then the stock VW versions. Contact points on the fuses, poor connections and thus, high heat, has been blamed for failures.
Other issues, such as bad cooling fans; which had bad bearings, causes high draws and heat, are another problem, causing damage. SO, there are a number of possibilities and all together; they, can cause melting issues, of wires and fuse boxes.
Watch this video; for testing and diagnosis of problem and how to make a new alternator charge wire:
If you don't want to make your own; Innovative Wiring Inc., can make you new wiring harnesses, which are MUCH better and superior, then the stock versions.
Here is info; on high quality aftermarket fuse boxes:
Standard Motor Products Inc. TechSmart™ Power Distribution Center
Other aftermarket versions of the fuse box; are made by Dorman and AutoKing with their "No More Breaking", line of auto parts.
This issue; has been discussed many times on this site, however I recommend following the testing and repairs, shown in the video and possibly, replacing your fuse box with a improved aftermarket version, if needed.
NewBeetle.org Forums - Search Results for melting fuse boxes billymade
Let us know; the results of your testing and how the new charge wire and fuse box replacement goes. After that; I would have the whole charging system tested and confirm; your battery and alternator are working as they should! Thanks!