HTX determines whether you have an invocation of Mosaic running by looking for the .mosaicpid file which it creates in your login directory and then checking that the browser process it describes still exists. This means that if you have more than one invocation of Mosaic running on the same machine, HTX will normally talk to the one you started most recently. If you run Mosaic on two machines that share the same .mosaicpid file, the results can be unpredictable.
If you open new windows from within Mosaic, HTX output will generally go to the most recently used one. This can sometimes make it difficult to use more than one window to view different documents, as HTX output tends to over-write whichever was used last. The best way of avoiding this problem is to start two separate copies of the browser.