To get a consistent workflow, you will have to make sure that all components have compatible versions.

In LRTimelapse you can set the Process Version in the settings.
If you use After Effects for RAW-File rendering, make sure to have the right Camera Raw (ACR) Version installed and the corresponding version of After Effects.

The following schematics will show compatible versions:

Lightroom 5 = ACR 8 (CC and CS6 with June 2013 update), needs LRTimelapse set to Process version "LR5/LR4"
Lightroom 4 = ACR 7 (CS6), needs LRTimelapse set to Process version "LR5/LR4"
Lightroom 3 = ACR 6 (CS5), needs LRTimelapse set to Process version "LR3"