I eventually got this to work, but I had to remove the tempdir argument to 3dttest++. However, I also had to ensure that AFNI_COMPRESSOR was not set as 3dClustSim could not read the -inset files if they were compressed. I got the following error:
[other output from 3dttest++ removed]
3dClustSim -DAFNI_DONT_LOGFILE=YES -inset .//resid.CStemp.L_whole_amygdala.3mm.???.nii -prefix resid.CStemp.L_whole_amygdala.3mm.CSim -LOTS -both -nodec -cmd resid.CStemp.L_whole_amygdala.3mm.CSim.cmd -mask ../mask.grey.mddAndCtrl.union.masked+tlrc.HEAD
++ 3dClustSim: AFNI version=AFNI_16.2.05 (Jul 22 2016) [64-bit]
++ Authored by: RW Cox and BD Ward
** ERROR: -inset './/resid.CStemp.L_whole_amygdala.3mm.???.nii': failure to open dataset
** FATAL ERROR: no valid datasets opened after -inset
** Program compile date = Jul 22 2016
** FATAL ERROR: ===== 3dClustSim command failed (( =====
** Program compile date = Jul 22 2016