Seee below for the issue:

Nov 3, 2013
As of Nov1-3 I worked intensively on the IST geometry and made a number of changes that should improve the Geant description and response.
- THE IBAM mother volume was changed into TUBS aka PXL 
- the IBMO was changed into a PCON to get rid of some ovelaps that could not be getting rid of
by shortening the lenght.
-Jason have checked the geometry and confirmed it matches the previous description for the IST ladder elements.
It should be commited and checked with simuation shortly.

This Change has dramatical improved the #steps in the IBMO volume.I suspect that all tracking issues in regards to IST in geant is resolved, and focus has to be on STI.
I think a similar change can be made to SSD and improve the steps there too. 
You can see the ladder volumes has been replaced by TUBS.

October 31

The issue of overlapping volums in IST is a problem for both geant tracking, but also for STI.
As of October 31, it looked like at least some issue were resolved by making IBMO 'ONLY' and setting its inner radius to
11.84 cm. 

It does though turn out that  this is not true away from the central region. The following geant3 figures show that volume
are masked (hidden) due to def of IBMO as ONLY out both in the east end and in the west end

Note e.g. the red part of support cone is maske by IBMO, as are several other parts. Likewise in the west end it also masks structures.
There is probably no need to have it this long, since the volume that belongs to IBMO does not extend quit so far.

The volume tree is here - Its essentially the ladder and parts of the cooling tubes.
All of these are well inside the current length of IBMO.
Changing the lenght from '20+Ladder_Lenght/2.0" to "12.957" fixes (almost) the problems described above and preserves the cables, placed well
within IBMO.
It does leave a small peice of a support Al ring on the MSC cut off See figure below note the green piece being identifed as air in ibmo whereas it should be Al in LFBA

In the final implementation the IBMO was changed into a PCON to avoid the problem just mentioned above (Nov2, 2014