Unanswered First layers too thick

Hi everyone,
I'm having a minor problem with my prints. The first few layers almost always come out too thick - you can see it in the attached photo (the part is supposed to be flat and not have the slight ridge on the left side). It's almost as if the extruder is squishing the first few layers into the bed, but if I raise the Z offset any further, the first layer no longer sticks to the bed and it starts printing in the air.
My printer is an R1+. I'm printing PLA with extruder at 212 deg and bed at 40 deg, using Simplify3D. I tried messing with the First Layer Settings (height/width/speed), G-Code Z-offset, and the offset in the starting script's M565 command with no luck. Any ideas about what else I can try to fix the starting layers?

 

Thanks for your reply. Here's my S3D startup script:
G28 X0 Y0 Z0
G1 Z5 F5000
M565 Z-1.1
G29

I was mostly using the Global G-Code Offset (Z-Axis) when experimenting with extruder offset from bed (AFAIK it has the same effect as modifying the z-offset in the M565 instruction). I didn't make large jumps, but rather changing the offset had no significant effect on the first layers being too thick: below ~-0.3 the extruder couldn't extrude the first layer, above ~0.2 first layer was not sticking, and anywhere in between - the first layer printed fine but layers 1-3 were too thick like in the picture above.

I wasn't using any adhesive on the bed. (I always use gluestick when printing a big part to avoid warping at the sides and popping of the bed, but I found that with small parts, the part will stick to the bed just fine on its own and it will have a nice shiny look on the bottom. With gluestick, the bottom comes out a lot more matte.) So could that be why my first layers are droopy?

I also noticed yesterday that the extruder is almost 0.5 mm closer to the bed at the center of the X-axis than on the sides. Is that bad?

 

I'm only seeing 5 projects listed there and nothing about updating Marlin. Is it on this site?

What's the difference between setting global z-offsets and the M565 instruction offset? I'm still a bit new at this

 

Thanks, I found it. I should use the lastest version (RCBF_MESH_PLUS_03-01) right?

It looks like a lot more work than I have time for right now so I'll probably try it over the weekend. Meanwhile, if there's anything else I can try to deal with the droopy first layers, please let me know.

 

You guys are not gonna like this - I'm now using my uneven bed as an excuse for not adjusting the Z-offset when printing small parts. In the center - great adhesion without gluestick. On the side - gluestick needed but no droopy start layers.

On a more serious note, will I void my warranty by messing with the firmware and is there a chance I can brick my printer if the firmware doesn't compile correctly? I've never worked with Arduinos or compiled firmware before.

Also, I still didn't get a reply on what the difference is between the M565 z-offset in the startup script and the global z-offset. Could someone please clarify this for me?