kbps is the amount of data sent per second, not the resolution of the file. FLAC is a lossless compression, so no matter the total weight and value in kbps, if your player says 16/44, then it is CD resolution.
the confusion here comes from how non PCM formats like mp3 or AAC use kbps to define compression "quality". they do that because not being PCM formats, they don't relate to notions such as bit depth and sample rate. so we use the next best thing kbps. but it is irrelevant for lossless formats like FLAC because those do have a specific way to define resolution, and that is your good old 16/44 for a CD.
as to why the kbps value can be smaller, it could be that the compression setting was set differently, or it could simply be that the music content was easier to compress in FLAC. don't bother with that.