I can find no mention of the tag "secret" in that rabbit warren we call the Trainz Wiki. Perhaps it was an old tag that has been replaced by the various "permit" tags now used in the Privileges container. However, in AssetX at least, the secret tag behaves as a Boolean variable, meaning it can only have values of 0 or 1. These correspond to "off/on" or "no/yes" according to convention.
It therefore struck me as odd that you could switch it off by changing its value from 0 to 1 because that's the exact opposite of the convention. When I checked my own copy of Shrub <kuid:-3:589>, I found the secret tag in fact had a value of 1, not zero, which explains its behaviour. Asset <kuid:-25:795> which obsoletes <kuid:-3:589>, also has secret set at 1, so I'm pretty sure it's 1 not zero in these assets. Is it possible you could have got the 1 and 0 confused? In any case, deleting a Boolean tag is usually equivalent to giving it a zero value, eliminating its effect, and that's what you found.
As to the flickering, I suspect it's another example of "texture fighting" caused by semi-transparent (blended alpha) textures being used on intersecting planes (classic "billboard" type vegetation asset). Trainz can't decide which plane should be in front of the other, so it flicks between them.
You might be able to reduce the flickering by telling Trainz to treat the texture as a "masked" instead of "blended" alpha;
Open the Shrub asset(s) for edit.
Find and open the file "flowers_yspots-flowers_yspots.texture.txt" in Notepad.
Change the line "AlphaHint=semitransparent" to "AlphaHint=masked".
Save the file and commit the asset(s).
This will change the appearance, but you would need to check how it looks in Surveyor to make sure it's acceptable.
The groundtexture "Shrub_grnd" has no alpha textures of its own, so it cannot cause the flickering, but it does call on the "Shrub" asset as a dependency to make a clutter mesh. If you manage to fix the flickering in the Shrub, it should also fix it in the ground texture/clutter mesh asset.
.
Mr R,
You were right about the "secret" value. 0 allows the item to be moved & deleted whilst 1 prevents those actions. Removing the "secret" line altogether from the config file allows the item to be moved, deleted or replaced.
The ground texture (shrub grnd,<kuid:-25:181>) containing the same yellow flower (which appears to be Flower Yellow Spots,<kuid:-25:518 albeit referenced via the scenery item shrub,<kuid:-3:589>) doesn't have the values you mention, in the "flowers_yspots-flowers_yspots.texture.txt" file. This txt file contains only the lines:
Primary=flowers_yspots.tga
Alpha=flowers_yspots.bmp
Tile=st
(Those referenced image files are contained in the folder with the config file).
I cloned the "shrub, grnd" groundtexture item and substituted a JVC grass scenery item for the flower-yellow-spots item, so see if this would work. It does - painting the texture on a bumpy landscape in Surveyor gives the texture with 3D grasses, instead of yellow flowers, scattered throughout and conformant to the bumps of the landscape. However, the same flickering problem persists.
The 3D items painted when the texture is painted will disappear altogether as you pull the viewpoint back, away from the area in which the texture is painted. You don't have to pull back very far for the 3D items to disappear (and re-appear when the viewpoint is once more moved closer).
In addition, moving the viewpoint about with the 3D items still visible causes them to jump about - as though they had been suddenly pulled into the ground only to instantaneously pop up again in different positions.
If I paint the 3D item as a single item from the scenery menu, rather than en-masse with the texture, from the texture menu, moving the viewpoint doesn't cause the 3D item to flicker in and out of existence, not change it's position. Therefore I conclude that the flickering is something to do with the way the texture references the 3D item, causing some sort of re-drawing of the 3D items as the viewpoint alters.
The shrub,grnd config file looks like this:
kind "groundtexture"
region "Australia"
obsolete-table
{
0 <kuid:-3:100310>
}
clutter-mesh <kuid:-3:589>
asset-filename "shrub_grnd"
username-cz "ker_zemní"
username-hu "shrub_grnd"
username-pl "krzew_podloze"
username-it "arbusti_terreno"
username-nl "shrub_grnd"
username-es "arbusto_suelo"
username-fr "Terre_buissoneuse"
username-jp "??_grnd"
username-de "shrub_grnd"
kuid-table
{
0 <kuid:-3:589>
}
kuid <kuid:-25:181>
Altering the referenced kuid for "clutter mesh" (in the original file or in a clone of it) allows different 3D items such as that JVC grass to be substituted for the yellow flower. But I presume something about the way the clutter mesh works is the cause of the above-described flickering ......................?
Any further suggestions for stopping the flickering will be gratefully received!

I would like to make textures containing landscape-conforming grasses and other 3D items. But not with the flicker in and out of the scene, as though they were holograms rendered by a faulty projector.
Lataxe