[Biopython] qblast results (NCBIWWW module) different from web blast results

[Alon philosof]

Hello all,
when I run a simple remote blast search using qblast of the biopython  
package i get different results from some sequences from what I would  
get for the same sequences when I preform
the search on the NCBI Blast web site. specifically, while the hit  
seems to be the same (same organism, protein and frame) the evalue is  
significantly  lower with the qblast.
needless to say I have used the same parameters for both searches.
interestingly, I encountered the same problem with the bioperl  
parallel module.
has any one noticed that?
any ideas how to solve that problem?

many thanks,

Alon philosof,
PhD student,
Prof. Beja's lab,
Technion - Israel Institute of Technology
philosof at tx.tchnion.ac.il