Hi Daffo123,
This reminds me a problem I encountered with gds export from Magma.
The problem may be unresolved cells or conflicting reference cells during gds export. Normally gds is merged using gds files of reference cells inside a design, e.g. macro gds files, standard cell gds files, analog cell gds files. Please check the log file to see if there are warnings during gds export phase, it can help you debug the problem.
If the problem is conflicting references, there may be 2 reference cells having the same name. This may cause the gds export command to choose wrong reference cells, and if both references are not the same size, you may end-up with overlapping cells.
If this is the case, you should modify one of your gds files and change the reference cell name. Then during exporting you should tell the tool to use that reference.
By the way, your case may not be the one I explained, but it sounds very similar and I hope it helps you,
Best regards,
Gokhan
---