Can you get version of standalone and rtabmap_ros like this:
$ rtabmap --version
$ rosrun rtabmap_ros rtabmap --version
To see if they have same dependencies (they should).
To know how exactly the parameters are called in rtabmap_ros, mouse over the checkbox in Preferences to show a tooltip with its code name. "Proximitiy in Time" would be RGBD/ProximityByTime, but there are more than one "Bundle Adjustment" parameter. If it is the one under Odometry panel (OdomF2M/BundleAdjustment), that parameter should be set to rgbd_odometry node, not rtabmap node:
$ rtabmap --params | grep Bundle
Param: OdomF2M/BundleAdjustment = "1" [Local bundle adjustment: 0=disabled, 1=g2o, 2=cvsba.]
Param: OdomF2M/BundleAdjustmentMaxFrames = "10" [Maximum frames used for bundle adjustment (0=inf or all current frames in the local map).]
Param: RGBD/LocalBundleOnLoopClosure = "false" [Do local bundle adjustment with neighborhood of the loop closure.]
Param: Vis/BundleAdjustment = "1" [Optimization with bundle adjustment: 0=disabled, 1=g2o, 2=cvsba.]
If you are not sure which node uses which parameter, set the parameter to both nodes. You can also do "rosrun rtabmap_ros rgbd_odometry --params" to see parameters specific to odometry, same for rtabmap node.
Note that replaying a rosbag could give slightly differences between runs, as not always the same frames will be processed.
cheers,
Mathieu