Ultrazynq MIO pins and JTAG EXTEST instruction

[Murphy86]

Have wierd issue where in some cases ultrazyng MIO pins are not acessible in EXTEST mode. (Not using vivado tools)
Regular FPGA IO pins work well, but EXTEST write operation on MIO pins have no effect.
Some boards work. When i compared jtag signal captured waveforms from working to not working, they are identical.
Bootmode set to jtag has no effect.
Has anyone seen this?
If so what was the solution?