Not quite sure what you've done with the skin options button, but try using this:
xml code:
<*PlusSkin Conditions(HideSkin = false) *>
<Button accvalue="Messenger Plus! CmdId: 7460" AccDesc="Skin Options" AccRole=57 Class="HIGToolbarButton" Layout=borderlayout() Active=3|4 Padding=rcrect("",20136)>
<ButtonIcon class="ToolbarIcon" content=rcimg("msgr",59006) ContentAlign=5 padding=rcrect("",20140)/>
</Button>
</*PlusSkin*>
in place of:
xml code:
<Button cmdid=7460 <*PlusSkin Conditions(SkinopsBtn = true)*>id=atom(SkinOpsBtn) </*PlusSkin*> AccRole=57 Class="TransparentButton" <*PlusSkin Conditions(AddSkinopsBtn = true)*>Layout=flowlayout(0,2,0,2) </*PlusSkin*><*PlusSkin Conditions(AddSkinopsBtn = false)*> LayoutPos=None</*PlusSkin*> Active=MouseandKeyboard|NoSyncFocus Padding=rect(5,4,5,4)>
<element class="ToolbarIcon" content=rcimg(59005)/>
</Button>
Also, do you really want to crowd the scene area with the extra scripts and skin options buttons?
Those are normally best off in the 1001 definition file.
Also, you haven't specified an image for the scripts button
And lastly I don't think you can/should remove the colourise button......it's hidden anyway by the curl in the top right hand corner and removing it might mess things up