Slow performance when backing up.

[inigoml]

We have experienced some troubles when performing a hot backup (Zimbra NE 4.0.X). In general, access is extremely slow, specially via web client (Outlook clients via ZCO and thunderbird users via IMAP4 don't show this problem).
Since most of our users access via Web, we only perform backup at nights, but since some users are world around sometimes there is no way to avoid this problem.
Is this performance problem a general problem or perhaps can be solved by tuning mysql/tomcat?
Our platform is a dual dual-core opteron (4 cores) with 4GB RAM, 4x150GB RAID10 SCSI disk and 300 users running RH ES 4.3.