Having a similar issue with a UP ready printer Ricoh IM C6010 where attempting to print a custom size will be sent to the printer as 8x11 instead of desired size (using Universal Print). This is even if you tell Universal print what tray to print to with the desired paper size. The normal print driver has 27 options for paper sizes (and works find if you send a custom size) the Universal print version only reports 11 very basic options.
I think customers would accept some compromises in advanced functionality but not being able to use enterprise printers to print on a variety of common paper sizes without any sort of workarounds forced us to rollback this deployment.
Universal Print options
Normal network print driver to traditional print server.