I think that the arrays might be something to do with it. by filling the script with prints, it shows that the $vec and $spli are pointing correctly, and is giving arrays ie:

libraries=ARRAY(0x8e04720)
vector_files=/home/sbi6dap/est2uni/data/vector.fasta
vector_info=ARRAY(0x8eefff4)
splice_files=/home/sbi6dap/est2uni/data/splice.fasta
splice_info=ARRAY(0x8e363c0)
[download]

But im not entirely (or slightly) sure where that leaves me. Also, for the record, the vec and splice files are definately in the right format and what the program is expecting.
Im going to get on the debugging asap, but if i dont go home and have some dinner first im going to starve to death or get locked in the building! neither of which sound fun on a friday night.
Thanks
Dan