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This seems to be a timing issue; ar_bounding box is running slow on your machine, thus some transformations are dropped. Some ideas:

• Try to increase the tf cache. In re_object_recorder/src/comthread.cpp, around line 59, change the ComThread constructor to e.g:

  ComThread::ComThread(QObject *parent) : QThread(parent), tf(ros::Duration(30.0))

• In re_object_recorder/src/comthread.cpp: Try to comment lines 115 - 129 out (this is a try-catch-block). This will disable storing the camera pose in the merged point cloud, which is not really necessary.