Sorry for the long time...
I made some tests with Ubuntu 8.10:
kernel 2.6.27-7-generic #1 SMP Tue November 4 19:33:20 2008 UTC i686

The problem still persists, but I don't think it is related to the patch 
attached early.
For every packet marked as invalid, the netfilter log reports:

ACK is over the upper bound (ACKed data not seen yet)

I can't understand if it is an error of netfilter or my network's problem.
I'll investigate.
Thank you

-- 
 netfilter: In TCP connection tracking, some valid packets are marked as INVALID
https://bugs.launchpad.net/bugs/264269
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