I edited the file to reflect some recent changes (%NAME% and %CLOCK% are gone)
More importantly, in your dualport template it seems clock1 is not used? This seems suspicious, could you try to add it back as in the dualport_bram_generic.v.in template?
Update ULX3S to enable selection of I2C pins, for the real time clock support.
Add "missing" dualport_bram_wmask_byte support.