Yo. I have confronted many people about this problem including SM Sith Lord.
Common charasterics I have ran into in the past of a 3DO not appearing are:
1. Template error
2. Sectors not selected right when converting to .3do
3. 3DO not set to sector placed in
4. Consistency Check Error
5. Thing limit has been reached

All of the above are perfectly fine, and I nor anyone I have asked has any idea what it could possibly be. There are about 5 of them that are not appearing out of the many. The weird thing is, I placed the SAME 3do thats not appearing only about 20 feet away, and that one DOES work. If anyone has any suggestions, it would be greatly appreciated. Ty.

I have had this problem with several of my levels in the past, once the number of 3do's started getting pretty big (but no where near the limit). I was never able to find a solution for this problem. I know other's have had the same problem, not sure if anyone has ever figured out the cause.

I have a similar problem, but instead of disappearing it turned into a thermal detonator. If anyone can figure out why his or my problem is happening, it would be GREAT.

I have had a problem similar to this.

I place a 3do, and its there for a fraction of amount of time, then i look somewhere, and then I look back and its COMPLETELY gone, as in not coming back. Its probably just the thing number... Place the disapearing 3do, some where uneeded, and just place the other 3do that doesnt disapear there.

tried it, didn't work

Hmms.

Some suggestions:

Is that disappearing 3do overlapping any other 3do?
( if so, move it even if by slightly .0005 so that it does not )

Is that disappearing 3do all in 1 sector?
( the only way that it can be in 2 sectors; is if part of the 3do is in water and it has a flag set for 'submerged' )

Confirm that the template 'size' and 'movesize' is large enough to include the longest dimension of the 3do
( so if you had a rope 40 long and .001 thick; the size should be = 40.0 and movesize 'at least' 20.0 )

Are all the surfaces of this 3do set with same flag?
( sometimes we can accidently set a surface side of a 3do to another value; or perhaps change its value inadvertantly )

If the 3do is exceptional large or complicated (such as an intricate tree; cleave it up into parts, but instead of merging them as 1 3do...simply highlight all of the parts and export as 1 3do)

Hmms.
If I think of any more suggestions, i will update this post.

G'luck on fixing the problem;
and if u do find a solution other than the ones suggested, please post what you did to fix the problem you have, so that it may help others.

Are the 3DOs that aren't showing up in multiple sectors? I've had a problem similar to this where 3DOs won't show up and they follow the specifications for having them show up. That's all that I can think of. Try placing the 3DOs in 1 sector (the starting sector of JED would work fine) and if none disappear, then that's probably the problem.

Yes, this sounds more like a sector problem rather then a 3do problem. Check for the following:

1) That the 3do isn't positioned on an adjoin.

2) That the flags in all of the sectors are the same.

3) That there are no sector cogs present (remove them for now to see if the problem resolves itself, if not, then you can put them back in).