Hi Corrie,
In the Edit Select Documents for Payment screen, you should be able to select all linked vouchers in that screen. I'm not sure why you can't - maybe you have a customization. I have tested in version 7.0 SP4, which shouldn't work any differently than SP3, and my linked vouchers are available for payment in the Edit Select Documents for Payment screen. The bug is that you should get a warning if you select a linked voucher for payment. So the fact that linked documents don't normally show in the PV list in your screen doesn't sound right to me. The fact that they now show does sound correct. Why they only show in that particular scenario is strange.
Is your Edit Select Documents for Payment screen customized? Or maybe the PV list has been customized.