Stamina,
It may be realated to your custom entities not being a saved in a compatible .x file description language.
Theres some variation in how differing progs generate the file format description on export depending on the model program used and the export filter and export settings used.
It may not in your case be this - but certainly incorrect file description or x.file errors can and does prevent entities from showing up in FPSC so it could be that.
If its not that then it may be that your entities are just being whisked away out of sight due to physics as you say its only dynamic entities it happens with. This can happen occasionally in FPSC due to mis behaviours of the program and once it happens its difficult to overcome as FPSC embeds info in the game file so it just keeps repeating the bad behaviours. It can happen simply by placing an entity somewhere that FPSC does not like it being and for no other reason. If this is the cause usually deleting the entities, exiting the prog and starting again placing entities in another position can overcome it.
If info gets embeded in the game then you may have to delete the entities .dbo and or .bin files before it will get removed and FPSC reset itself. Dont forget - dont delete anyhing unless you got backups.
It may be the positioning of the centre axis point of a model as created in a modeller - I always move my models up in modeller so that their base is just above the centre line of my model prog.
None of that may help but they are some things that have caused me problems in the area of entities not being visible.
I have personally never had that problem and found it being related either to the FPCS version or my video card(s)
Obviously your models should not be invisible so there is a reason for it - which if you can isolate it by eliminating possibilities will give you a fix.
Trouble is there could be numerous and a combined number of reasons for this happening.
"I am and forever will be your friend"