Can you check you vnc log and look for this: "Underlying X server release 70200000, The X.Org Foundation" - see what version you see...
Also, verify that the only change you made to the ebuild is the XSERVER_VERSION="1.3.0.0" line, right?
It should then pick up xorg-server-${XSERVER_VERSION}.tar.bz2, and this is the code that the vnc-4.1.2-r4-patches-0.1 file will try to patch. These two seem incompatible entirely... See if, while emerging, you see these exact files being unpacked, etc.
Can you check you vnc log and look for this: "Underlying X server release 70200000, The X.Org Foundation" - see what version you see...
Also, verify that the only change you made to the ebuild is the XSERVER_ VERSION= "1.3.0. 0" line, right?
It should then pick up xorg-server- ${XSERVER_ VERSION} .tar.bz2, and this is the code that the vnc-4.1. 2-r4-patches- 0.1 file will try to patch. These two seem incompatible entirely... See if, while emerging, you see these exact files being unpacked, etc.