When you want to make a map, there is 2 possible edition mods: the "edit mode" and what I would call the "usable" mode. When you start your map, you will have to choose between all the classic mods (capture the flag, siege, commander battle...), that's what I call the "usable" mode. You will use this mode to test your map. But there is also a last option called "edit mode", made specifically for editing your map.
The "edit mode" is made for editing, while the "usable" is made for testing. Why? Because all interactive props that you see in "usable" mode are NOT those that you set in edition mode. Basically, if you set a cannon in edit mode, when you go in usable mode you will see that your actual cannon (a bit bigger) is placed at -30000 under the ground, and was replaced by a usable cannon with different parts. That's the same for the flag. The entry point 66 is replaced by a banner pole (spr_headquarters_pole_code_only) and a flag (spr_headquarters_flag_swadian). Moving those objects is pretty pointless as they are not integrated in your map but generated at game start.
So your problem there is that, instead of using the "edit mode" you used the "usable mode". Now just go in "edit mode", find entry point 66 or create one (it corresponds to your flag) as Conway said.
By the way, for a siege map, don't forget that at the beginning of the round, all players will spawn at entry point 0 (defender) or entry point 32 (attacker). Therefore place those entry points in an open space with enough room for everyone.