Generally, Adobe Media Encoder should not render an old version of your After Effects composition, but there are some circumstances that could cause this. To explain why, I’ll detail some of the under-the-hood details of how Adobe Media Encoder and After Effects interact:
1. In After Effects, the Composition > Add To Adobe Media Encoder Queue command saves a copy of your project in a temporary folder (compositionName_AME, saved in the project file directory), and this is the project that is sent to Adobe Media Encoder. This also occurs when you drag a composition from the Project panel in After Effects to the Queue panel in Adobe Media Encoder.
Because this temp project is separate from your original project, changes you save into your project are not reflected in the temp project. Therefore, if you make changes to your project, you should not reuse an instance of this temp project in Adobe Media Encoder’s queue. Instead, use the Add To Adobe Media Encoder Queue command again to send a fresh copy.
2. In Adobe Media Encoder, you can also add compositions by using the File > Add or Add After Effects Composition commands. The Add dialog can also be invoked by double-clicking in the empty space in the Queue panel.
This method will reference your original project file, no temp projects are involved, so changes you save into your project will be reflected.
However, once Adobe Media Encoder has loaded a composition into memory, it will not refresh it after you save changes into the project. This is a bug. To work around this problem, quit Adobe Media Encoder, wait about 5-10 seconds to allow all of the sub-processes to shut down, then relaunch Adobe Media Encoder. (This may not be necessary 100% of the time, as when Adobe Media Encoder runs out of memory it will close unused sub-processes automatically, and reload them when you request their use again.)