> I know this is an unusually large file
> (over 1000 lines, around 60k) but I could think of no
> other way to mirror this site.

Hum, okay, problem found: for each URL added, the 
engine always store a 'a priori' +<URL>* default 
filter - and therefore the internal filters table, 
limited to 500 entries, overflowed.

Therefore you have to increase it - this is possible 
using an option:
-#F3000

This should be fine (put this option after your URLs 
or in the filters section)