The WinSXS folder is not designed for MSIs Installers.
That is more a Windows managed directory.
I would recommend updating your MSI Installer to not install to the WinSXS directory.

For Capture, Make sure the software is not already on the machine.

However, it is generally far better to automate the Vendors Installer (Likely Created with InstallShield) than try to capture and push.
(The actual MSIs will likely be dumped in a Temp Folder that can be grabbed if you pause part way through a manual install...but even this would not be a supported install since you may lose custom ISS scripts.)
The capture will grab a lot of junk and lose all intelligence.
Further, the software vendor would never support the product installed in such a fashion, since they would have no way of knowing if it was installed properly.

Perhaps using InstallShield to capture options to build an MST may work.