No, such switches do not normally happen. Did you specify in any way that you have D-amino acids in you system? This is necessary - even though the standard terms in the force field are symmetric wrt L- and D-amino acids, the CMAP cross terms are different and so you need to use toppar_all36_prot_c36_d_aminoacids.str and the residue names in it; this is in CHARMM, I have no idea about CHARMM-GUI or GROMACS.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden