Right figured this out, sorry my fault it wasn't actually a transmission issue (that was set to 1, I must of been fiddling with it when I took the screen shot). So the issue did occur even with a transmission of 1.
The problem was I think with everything being a bit flat. So I added a few edge loops and added a bit of curve to the base, making it more parabolic(?). Also, made sure I didn't have any extra faces hidden in the base.
Also used all the setting recommended above (thanks everyone, much appreciated) ie.
- blend type to "Alpha Blend" in settings for the material
- See if mesh object doesn't have negative scale and has its normals calculated inside
- “screen space refractions” turned in settings for the material