I got your message. I like your timeline figure, but just redrew it to show what might actually happen. There are a few things for you to know, to understand how MultiTarget (or SingleTarget) works.

MultiTarget (and SingleTarget) does not change its fixation status until the tracker remains in the target window for one entire frame. It means that, even though the eye crosses the threshold window sometime during Frame 0, the adapter does not think that the fixation is made until the end of Frame 1. So counting HoldTime starts from the beginning of Frame 2. The reason for doing this is to prevent a jitter from being detected as a fixation. It is also because the eye is still moving at the time of window crossing and the actual fixation does not start from that moment.
Choice2 AcquiredTime can be earlier than Response1_End, if the eye is already in the target window before the scene starts, as drawn in the above figure. In that case, the RT property of MultiTarget becomes 0, since the fixation is not a reaction to the targets. Note that the data collected during the last frame of Choice1 is analyzed at the beginning of Choice2.
https://monkeylogic.nimh.nih.gov/docs_CreatingTask.html#RuntimeVersion2_BackgroundThe targets turned on during Choice1 are turned off at the end of Choice1 but the screen is not updated until the first frame of Choice2 (Response2_Start). So Response2_Start is the time when the subject sees the removal of the chosen target. The unchosen targets in Choice1 are turned on again before Response2_Start so that they appear to exist continuously.
The actual hold duration may not be exactly 400 ms. Please see
this post for the details.
To answer your question, the reaction time for the second choice should be (Choice2 AcquiredTime - Response2_Start). The cue for the second choice in your task is that the target chosen from Choice1 disappears, which is timestamped by Response2_Start. The AcquiredTime sometimes being earlier is just because your subject makes estimated saccades before the chosen target disappears. You need to vary Choice1 HoldTime so that it is hard for the subject to guess. Or skip the reward if the AcquiredTime is earlier than Response2_Start.