Hello,
Using 3dWarp and align_epi_anat.py shouldn't put everything into common space. AFNI uses the +tlrc to signify ANY common space (MNI, TLRC, HaskinsPediatric, etc). It could be that one of your anatomical files is incorrectly reporting the space that it is in and that may be causing a problem. Also, you shouldn't have to deoblique the data before alignment, align_epi_anat.py should do this for you. Let's start with these three questions:
1) What is your original align_epi_anat.py command?
2) What is the output of afni_system_check.py -check_all
