The pgm_read_*_far() functions manipulate the RAMPZ register but do not restore it when they are finished.

This behavior is usually safe for any part with 64 KiB or less of data memory address space, because the RAMPZ register is only ever used in relation to the ELPM instruction.  Saving and restoring the RAMPZ register would normally be an unnecessary waste of cycles and Flash in such circumstances.

However, with the ATxmega series of devices, the RAMPZ register is also used every time any indirect data memory access happens through the Z pointer via the normal LD and ST instructions.  As soon as one of the pgm_read_*_far() functions is invoked, the RAMPZ register will be left in a modified state, rendering any subsequent compiler-generated indirect access of data memory through the Z pointer invalid.  This also makes pgm_read_*_far() interrupt-unsafe on such devices.

Possible fixes include:
1) Modify the pgm_read_*_far() functions to save and restore the RAMPZ register if the functions are used in a device which also uses RAMPZ as part of its normal indirect data access.
2) Modify GCC so that it never uses the Z pointer to indirectly access data memory on a device which also uses RAMPZ as part of its normal indirect data access.
3) Modify GCC to set the RAMPZ register appropriately (initially this might mean simply zeroing it) every time it begins accessing data memory through the Z pointer on a device which uses also RAMPZ as part of its normal indirect data access.