I'm in agreement with Scott - shared points between runs is likely the culprit here.
With multiple runs that have shared/repeated observations, the proper method to get final values would be a network adjustment rather than trying to daisy-chain the runs together - especially if they weren't done in a very regimented way that allows successive runs to build off of earlier runs.
Import the level file, make sure the "allow network adjustment" radio button is selected, QC your point IDs and misclosures. Uncheck the Create column for turn points. Then click OK and run a network adjustment using the resulting level observations. Ignore the "Adjust Runs" button and be sure to properly apply the correct standard error (by distance or by turns).
I haven't used the Adjust Runs button for years now; everything I do is network adjusted with levels + TS + GNSS which allows for far better blunder trapping and statistical analysis. Incorporating properly weighted level observations really helps to isolate potential issues with height/measure ups. Even if I'm only processing levels, they get a network adjustment.
------------------------------
Eric Glaves
------------------------------