I'd say yes it flags it because of CTM.
The 'infected' sectors clearly show CTM_ loader is there, the rest is crypted.
0000 FA E9 EB 00 F8 EC 68 23 43 54 4D 5F 00 00 00 00 úéë.øìh#CTM_....
Normally MBR infectors cause issues when overwriting existing changed MBRs, take a Truecrypt MBR or a CTM MBR it would break TC or CTM.
If a TC MBR is changed you can't boot your system and if a CTM one is I think it won't boot or else at least the 'home' button feature should fail to work.