Okay, the problem is threefold:
1. Your transparent color seems to not have been palette index 255 (very last color spot on the palette). This can happen if you use black as your background as the index conversion may choose a different duplicate as your color. You can use Wally to swap the indexes, or HL-Texture tools to pick it. Also the best bets to go with when making your transparent color are RGB 0 0 255 or RGB 0 255 0.
2. You saved the wrong format. Masked transparency is "AlphaTest". Your sprite format was "indexalpha" which is a totally different type of transparency used for decals and is the reason why it showed up as a black square in VHE
3. Stuff like plants/trees that stand upright or have a part that should be planted in the ground should be using "Parallel upright" instead of regular parallel (which can look like the plant is uprooting itself at angles).
Sprites can be pretty annoying assets to make and understand, I made a corrected version here:
http://www.the303.org/stuff/plant.rarAlso I wrote a big tutorial series on these:
http://www.the303.org/tutorials/gold_sprite.htm