Hi David,
This is a limitation in STAAD.Pro. Any LIST command can hold up to a certain number of entities. When the file is saved using the GUI, the commands are written in the command file in such a manner that this limit is not exceeded. If more than the permissible number of entities are found, the command is broken down into multiple commands. However the software is able to consider all the assignments correctly and this splitting of command does not have any bearing on the analysis/design results.
One of the inconveniences caused by this splitting is that there could be multiple references ( like say R1 , R2, R3 etc. for member properties ) created for the same property. The menu option Tools > Merge Properties can be used to merge such references.