Fragment Size shift on Egel bye using the new TruSeq protocol ?

[Claire1]

I am using the TruSeq protocols for RNA and DNA and I follow exactly the protocol, except I’m using an Egel (Egel: Invitrogen ‘Size Select’ 2%, Ladder: Invitrogen 100bp, 20ng/ul) before PCR instead of an Agarose Gel.
If I take my fragment size I want to use e.g. 600bp for my PCR and I run a Bioanalyzer after I see fragments around 500bp. So I have always to repeat my PCR's taking fragments around 700bp or higher to get fragments around 600bp.
This phenomenon I can see for DNA and RNA.

Anybody knows this problem?
Should I use a different Ladder?
Is the new adapter changing the migrating in the Egel?

thanks a lot for your help!

[JHU-ChIPmaniac]

I replied on your other thread.

[nilshomer]

Yes, please do not duplicate post.