Same serial command, different serial replies
A serial interface, even a standard one like RS232,  enforces nothing about the application protocol (available commands and their syntax) of a device. Which can have all kinds of special cases and commands that change settings or the way other commands work, limited only by the creativity and/or masochism of the engineer that designed it. This is why the same command can give you different results. Sometimes commands need other commands or conditions to provide results you are looking for.

As a metaphor, on a command prompt on your PC, typing ls will give you a different result if you issue a cd command to change directory in between. This is an illustration of how a command can have a side effect on the output of other commands. 

In this particular case, there is something either the application or device is doing that provides valid data in one case but not the other. Or something you are missing in the capture, or even something you physically do to the device (e.g. power cycle, or button press) that you did not account for. 

That being, this is simply the "joy" of reverse engineering, figuring out all the little details and side effects. It is impossible for anyone to give you any more information without either providing more information on the device, but even then all we can do is guess unless you can find command documentation or a protocol specification for this device. Sometimes this is provided in a datasheet or manual even if proprietary software is available as well, so it is worth checking.