Update: You were right; it was a memory problem running 3dttest++ on the command line. I submitted the code via the sge scheduler and eventually got it to complete after increasing the memory limit. However, now there are no more significant voxels :(
The exact command that I used was
3dttest++ -prefix stat.6.covary_ACM -AminusB -setA Vrel FP OLSQ.FP.betas+tlrc.HEAD[Vrel#0_Coef] FR OLSQ.FR.betas+tlrc.HEAD[Vrel#0_Coef]
FT OLSQ.FT.betas+tlrc.HEAD[Vrel#0_Coef] FV OLSQ.FV.betas+tlrc.HEAD[Vrel#0_Coef] FX OLSQ.FX.betas+tlrc.HEAD[Vrel#0_Coef]
GF OLSQ.GF.betas+tlrc.HEAD[Vrel#0_Coef] GG OLSQ.GG.betas+tlrc.HEAD[Vrel#0_Coef] GI OLSQ.GI.betas+tlrc.HEAD[Vrel#0_Coef]
GK OLSQ.GK.betas+tlrc.HEAD[Vrel#0_Coef] GM OLSQ.GM.betas+tlrc.HEAD[Vrel#0_Coef] -setB Arel FP OLSQ.FP.betas+tlrc.HEAD[Arel#0_Coef]
FR OLSQ.FR.betas+tlrc.HEAD[Arel#0_Coef] FT OLSQ.FT.betas+tlrc.HEAD[Arel#0_Coef] FV OLSQ.FV.betas+tlrc.HEAD[Arel#0_Coef]
FX OLSQ.FX.betas+tlrc.HEAD[Arel#0_Coef] GF OLSQ.GF.betas+tlrc.HEAD[Arel#0_Coef] GG OLSQ.GG.betas+tlrc.HEAD[Arel#0_Coef]
GI OLSQ.GI.betas+tlrc.HEAD[Arel#0_Coef] GK OLSQ.GK.betas+tlrc.HEAD[Arel#0_Coef] GM OLSQ.GM.betas+tlrc.HEAD[Arel#0_Coef]
-paired -covariates covary.toe.gap.txt -ETAC -ETAC_blur 0 4 -ETAC_opt sid=1:hpow=0:name=test1:pthr=0.01/0.001/10:fpr=9
-mask mask+tlrc
The purpose of this was to test if the issue can be replicated on your data with blurring. I will try hpow=2 to check significance but if there's no voxels significant, it makes it very difficult to debug if the same exact settings can't be tested for both datasets. :(