First layer settings ignored

[craftyham]

Hello everyone,
So everything has been going well until the other day. S3D seems to be skipping my first layer settings, including layer height, & temperatures & fan settings. It seems to be treating the prime line as layer one, & the temperature presets i added to the start code are not being followed. At the Start of a print it starts heating the bed to the second layer setting, Then, disregards the the first layer settings after the Prime line and starts printing at layer two, it also isn't printing the skirt like it normally does either. At the moment it doesn't seem to move past heating the bed up either. Even with the M-code removed from the start script it is still skipping layer one presets, even before it does the prime & wipe line<--only thing that is being followed other then the nozzle temperature.

Thank you in advance to anyone who helps me get back to printing again.