This is my test case for merging multiple and back shots. It works. Could you send an example of your issue?
# 2016.12.11 created by TopoDroid v 3.1.6a
# test
# from to tape compass clino (declination 0.0000)
# units tape meters compass clino degrees
0@höhle,1@höhle,9.17,120.87,-14.4
1@höhle,-,5.00,140.87,0.0
2@höhle,-,5.00,140.87,0.0
1@höhle,2@höhle,5.30,144.87,5.4
2@höhle,1@höhle,5.27,334.87,-8.4
1@höhle,2@höhle,5.20,164.87,10.4
1@höhle,-,5.00,160.00,0.0
2@höhle,-,5.00,150.00,0.0