Will I still get flagged for missing my height and weight, even if I pass my PT test?

Soldiers are required to conduct HT/WT every 6 months at a minimum, but the Commander of a unit can order Soldiers at any time to conduct HT/WT. The only time you do not have to get HT/WT is if you score 540+ (min 80 points in each event). Your 538 means you get HT/WT and taped.

If you fail the tape, then yes you will be flagged. If you purposefully try and skip the HT/WT, then yes you could be flagged because you could be facing some sort of administrative action.....like an Article 15 for disobeying a direct/lawful order.

Yes - or at least this was the case when I was in. Height/weight requirements are/were independent of your physical fitness.

Everyone is required to be within standards. Height and weight is a requirement with exceptions. As MSgt Livingston said if you have 540 plus as your score you get a pass. You didn't. If you fail height and weight the tape is an exception to help you out. If you fail height/weight and also fail tape then anyone would get flagged. If you are going to school you will need to have this under control because I assume they will test you at school and do height/weight while there.