While the uBlox Neo-7M GPS modules are pretty easy to use, they only have an internal ROM. If you want to load a different configuration on these modules (which you need to get a 10MHz square wave out), that configuration has to be stored on an external flash EEPROM.

The eBay module actually has an EEPROM on it, no issues there. The problem is that these modules "forget" to use the externally stored configuration after the backup power supply has been removed or dropped too low. For this purpose the eBay modules have a supercap on the battery backup pin, but it discharges to fast and the configuration is lost after a couple of hours of being unpowered.

Although I am pretty swamped with university work at the moment I did manage to solder on a diode and double AA battery holder onto the module in order to retain the configuration.

I assume the problem is, that the module's firmware has a flag in SRAM which it checks and then decides whether to load the config from internal ROM or external flash EEPROM. Once the battery backup power is removed, the SRAM loses it's contents, therefore resetting the configuration. The config isn't really lost, the module just doesn't know to load an external config.