This is normal. It is because of the first layer thickness setting. Since your first layer is 0.25 mm thick, the printer moves to 0.25 mm above 0.
If your printer is printing too high for things to stick to the bed, then you should not adjust this setting. Instead, you should either relevel the bed or use the baby stepping controls to adjust the printing height on the fly.
Yes such as Solidwork. On the save as screen when you select the STL format there is an options button. If you designed in millimeters and export is set to inches you will import the model expecting a millimeter file unknowing the software used converted and save as inches. This would make for a very small model.
I just tried to reproduce your problem, and Export to X3G displays just fine on a fresh Replicator 2 profile. My guess is that somehow under SETTINGS > Printer > Features, the Sailfish Communication box came unchecked, as that is the setting that triggers whether or not the Export as X3G option appears in the QUEUE menu.
MatterControl only has EEPROM mapping for printers running Marlin or Repetier firmware. Your printer is probably running a firmware which MatterControl does not recognize. You can still change the settings you need to, but you will have to do it by hand through the G-Code terminal. See the RepRap wiki on using the M503 and M500 commands.
On Arch based distros make sure you have installed mattercontrol-plugins as well. This has the closed source plugins including the S3G driver for Flashforge printers. Also make sure you have given your user permissions for the serial port. See the wiki article on running on Linux.
So having separate temps for the first layer doesn't make any difference in prints? I was just curious about using it because others I know use Simplify3d and it allows them to select different temps for different layers. Most use a higher temp for the firs t3 layers then drop it down and start the fan. I assumed there was a good reason for it.
It is caused by the fact that MatterControl does not send a single move command but instead breaks up the move into smaller segments. This allows us to do some things that other software can't (like print leveling and babystepping), but one of the side effects is that stutter when jogging. We're thinking about adding a way to disable the move segmentation in the next version.