That is intended, placed items are not saved unless they are within 50m of a flag. This reduces Lag as well as the size of the save file.

Aw right, I just wish they would stay but oh well, thanks anyway!

@Civil Garrisoning troops in town are nice but not crucial really. At most they can help ward off the odd patrol at certain locations. I personally am wary of garrisoning the towns as I prefer not to have the cities used by AIs as a battlefield. I constantly worry the enemy faction might bomb them and add more civ casulty. Another important thing is if your town flips to enemy faction, you loose that garrison.

If you really want a garrison, just don't be within spawning range of it. The garrison will be there theoretically but nothing will spawn in for civis to run over.