Since you appear to be able to configure the Venus GPS successfully and get it working as to how you want it to operate, but cannot get it to remember settings after a power cycle then it sounds like there is something wrong with the flash writing procedure.
The only thing I can think of that would cause the write to flash procedure to fail is lack of power going to the chip.
How are you powering the Venus? If its via the
FT232RL breakout then I believe it barely has the amperage to power the GPS alone much less the required power for the flash write procedure.
For example say it takes 10mA to read a flash chip then most likely it'll take 80mA to write to it or more. That is just an example, I haven't actually measured a flash chip during a write vs a read. But I do know that from previous experience and reading various flash chip documentation the power requirements are quite a bit higher during a write than a read.
The really bad part is that SkyTraq hasn't given us any power requirements for their GPS chip except during power-down mode for the battery operated save of the SRAM which is 10uA. I've read somewhere it appears to have a <80mA power usage during start time and goes to like 40mA during normal runtime. It would be nice to have the power figures from the vendor themselves though.