[Touch Dual, MDA Touch Plus ROM Development] hiffy:
your HTCHomeSettings.xml file doesn't match the Weather image files you are using. the position of your weather icons is different to the position on the default Lilly theme so i'm guessing that M2DC has modified them, but the theme doesn't come with weather image files. If you want to use your new theme but keep the default weather images then you'll have to modify you HTCHomeSettings.xml file manually. Try Diff'ing your file with the default Lilly one and see what the differences are. the group of properties you'll need to edit look something like this:

<WeatherWidget>

<Property name="IDWEWG_LASTUPDATEBTN_RECT"	id="0" value="160,40,70,15,147,40,151,15"/>

<Property name="IDWEWG_WEATHERBTN_RECT"	id="1" value="4,47,232,60,4,47,312,60" />

<Property name="IDWEWG_LOCATIONBTN_RECT"	id="2" value="4,51,232,200,4,136,312,23" />

<Property name="IDWEWG_STATUSTXT_RECT"	id="3" value="15,91,210,60,15,51,290,60" />

<Property name="IDWEWG_LOCATIONTXT_RECT"	id="4" value="15,121,210,22,15,136,290,22" />

<Property name="IDWEWG_LASTUPDATETXT_RECT"	id="5" value="156,50,82,15,147,40,151,15" />

<Property name="IDWEWG_ADDCITYTXT_RECT"	id="6" value="15,51,210,60,15,51,290,60" />

<Property name="IDWEWG_ARROWTXT_RECT"	id="7" value="0,28,10,13,0,28,10,13" />

<Property name="IDWEWG_TEMPERATURETXT_RECT"	id="8" value="8,33,80,40,15,33,80,40" />

<Property name="IDWEWG_DOWNARROWRELEASE_IMGID" id="9" value="83" />

<Property name="IDWEWG_DOWNARROWPRESS_IMGID"	id="10" value="82" />

<Property name="IDWEWG_REFRESH_IMGID"	id="11" value="84" />

<Property name="IDWEWG_SEPERATELINE_IMGID"	id="12" value="86" />

<Property name="IDWEWG_DOWNARROW_POS" id="14" value="216,116,307,74" />

<Property name="IDWEWG_UPARROW_POS"	id="15" value="216,90,300,74" />

<Property name="IDWEWG_REFRESH_POS"	id="16" value="220,116,300,10" />

<Property name="IDWEWG_WEATHER_POS"	id="17" value="58,15,165,25" />

<Property name="IDWEWG_SEPERATELINE_POS"	id="18" value="0,210,0,210" />

<Property name="IDWEWG_HIGHTEMPTEXT_TODAY_RECT"	id="19" value="8,78,60,15,8,78,60,15" />

<Property name="IDWEWG_LOWTEMPTEXT_TODAY_RECT"	id="20" value="8,93,60,15,8,93,60,15" />

<Property name="IDWEWG_DAYTEXT_WEEK_RECT"	id="27" value="0,4,100,12,0,5,100,25" />

<Property name="IDWEWG_HIGHTEMPTEXT_WEEK_RECT"	id="28" value="0,0,26,15,175,5,30,15" />

<Property name="IDWEWG_LOWTEMPTEXT_WEEK_RECT"	id="29" value="0,0,26,15,210,5,25,15" />

<Property name="IDWEWG_SEPERATELINE_IMGID_P"	id="30" value="116" />

<Property name="IDWEWG_SEPERATELINE_POS1"	id="31" value="47,143,47,145" />

<Property name="IDWEWG_SEPERATELINE_POS2"	id="32" value="0,166,0,168" />

<Property name="IDWEWG_LOCATIONINDEXTXT_RECT"	id="33" value="205,100,34,20,0,0,0,0" />

<Property name="IDWEWG_FORECASTCONTROL_RECT"	id="34" value="0,0,0,62,0,0,0,62" />

<Property name="IDWEWG_LASTUPDATETITLE_RECT"	id="35" value="135,38,105,15,147,40,151,15" />

<Property name="IDWEWG_SEPERATELINE1_IMGID"	id="36" value="197" />

<Property name="IDWEWG_SEPERATELINE2_IMGID"	id="37" value="198" />

<Property name="IDWEWG_WEATHERTEXT_RECT"	id="38" value="0,141,240,22,15,136,290,22" />

<Property name="IDWEWG_UPARROWRELEASE_IMGID" id="39" value="85" />

<Property name="IDWEWG_UPARROWPRESS_IMGID"	id="40" value="84" />

</WeatherWidget>

The values are the screen positions for icons and text on the weather tab. Compare your file to the default Lilly file.

Note that the above extract from a HTCHomeSettings.xml file is just an example and not the from default Lilly file. Also, the way in which M2DC applies themes isn't perfect and you may need to do manual mods like this if the default theme in your ROM is not the same as the default them in the Manila2D package.