So, at least you know you aren't alone. I'm having the same bug, as well as the OP in the thread I just linked. I can post images, as well as my stats, hopefully this helps. First, the images: I'm using the mk1 and the lander can as good examples, but it happens with every crew module I use.
I have crew in the module, and can fly/use parts; however,
I have no crew portrait.
I'm running:
Operating System
Windows 7 Ultimate 64-bit SP1 CPU
Intel Core i5 2400 @ 3.10GHz
Sandy Bridge 32nm Technology RAM
8.00GB Dual-Channel DDR3 @ 665MHz (9-9-9-24) Graphics
NVIDIA GeForce GTX 660 (EVGA)
KSP version:
1.1.3.1289
Mod list:
B9 Aerospace (Parts v6.1.2, Props v6.1.2, Modules v1.0.3, Part Switch 1.4.3)
CapCom Mission Control On The Go v2.4
Community Resource Pack v0.5.4.0
Contract Configurator v1.15.5
Contract Pack: SCANsat v0.6.0.1
Contract Parser v4.0
Contract Reward Modifier v2.3
Contracts Window + v6.4
DMagic Orbital Science v1.3.2
Firespitter Core v7.3.0
HyperEdit v1.5.2.1
Interstellar Fuel Switch Core v2.1.1
MechJeb 2 v2.5.8.0
Mechjeb Embedded Universal (It's Free!) v1.3
Module Manager v2.6.25
Near Future (Construction v0.6.4, Electrical v0.7.7, Electrical Core v0.7.7, IVA Props v0.5.1, Propulsion v0.5.1, Solar v0.6.2, Solar Core v0.6.2, Spacecraft v0.5.1)
Prakasa Aeroworks v0.5.0
Progress Parser v5.0
Raster Prop Monitor 1:v0.27.0
Raster Prop Monitor Core 1:v0.27.0
SCANsat v16.3
SmokeScreen Extended FX plugin 2.6.17.0
Station Science v2.0
TweakScale - Rescale Everything! v2.2.13
If that doesn't help pin it down, I don't know what will.