Alignment issues when hovering over header

I am seeing wierd alignment issues when hoverign over the header of a dhtmlxGrid.
I am using Ie9 in ie9 doc standards mode. Dont see this issue with same code when running in IE9 with doc standard 7. Running with dhtmlx suite 3.6

I use a bunch of checkboxes which are enabled by default(to show all columns). When i uncheck the check boxes it makes call to setColumn hidden and hides the columns. On initial load there are no alignment issues when i hover . When i uncheck a check box and start hovering the header columns expand in height.(I am unable to add the screen shots here for some reason)

Any help is really appreciated
IE verion is 9.0.8112.16421
Note that this behaves fine on other browsers but the cutomers use this specific version of Ie.

Relevant piece of code and values in js variable at that point

var mygrid;

var formData = '[{type: "settings",position: "label-right"},'; 
var lenSubHead = subHeadNmArr.length;
for(var p=0; p<subHeadNmArr.length; p++){
	formData += '{type: "checkbox",label: "'+subHeadNmArr[p]+'",value: "'+subHeadStartArr[p]+'",checked: true}';
	if((p+1)%2 == 0 && p != (subHeadNmArr.length-1)){
		formData += ',{type:"newcolumn"}';
	}
	if(p != (subHeadNmArr.length-1)){
		formData += ",";
	}
}
formData += "]";

var myForm = new dhtmlXForm("myForm", eval(formData));
myForm.attachEvent("onChange", function (id, value){
	for(var q=value; q< (parseInt(value)+ parseInt(subHeadLenArr[value])); q++){
		mygrid.setColumnHidden(q,!myForm.isItemChecked(id));
	}
    return true;
    //alert(id+'::'+value);
});


mygrid = new dhtmlXGridObject('gridbox');
mygrid.imgURL = "/itsc3/dhtmlx/dhtmlxGrid/codebase/imgs/icons_scorecard/";

//mygrid.kidsXmlFile="it_scorecard_lev1.jsp";
mygrid.kidsXmlFile="/itsc3/getmetricdata.do";
//mygrid.setHeader(colStr,null,eval(colLabelStr));
mygrid.setHeader(colStr0);
mygrid.attachHeader(colStr1);
mygrid.setInitWidths(initWidthStr.substring(0, initWidthStr.length-1));
mygrid.setColAlign(colAlignStr);
mygrid.setColTypes(colTypeStr);
//mygrid.setColSorting(colSortStr);
//mygrid.setMathRound(2);
mygrid.setStyle("color:black;font-weight:bold;text-align:center;vertical-align:middle;word-wrap:break-word;","border-style:solid;border-color:#d3d3d3;border-width:1px;","font-weight:bold;","font-weight:bold;");
mygrid.enableMarkedCells(true); 
mygrid.init();
mygrid.enableRowsHover(true, "hover");
mygrid.setSkin("dhx_skyblue");
//mygrid.enableHeaderMenu("false,true,true,true");
//mygrid.loadXML("it_scorecard.xml");
mygrid.loadXML("/itsc3/getmetricdata.do");
mygrid.setEditable(false); 
mygrid.enableAutoHeight(false);
mygrid.enableAutoWidth(true);
	
//mygrid.splitAt(1);
var adjustColFlag = false;
mygrid.attachEvent("onXLE", function(){
	if(mygrid.getRowId(0) == "1~21873844_21873844"){
		mygrid.setRowColor(mygrid.getRowId(0),"#fff0f0");
		mygrid.setRowTextBold(mygrid.getRowId(0));
	}
	document.getElementById("btn_apply").disabled = false;
	if(adjustColFlag) {
		for(var q=1; q<colCount; q++){
			mygrid.adjustColumnSize(q);
		}
	}
	adjustColFlag = false;
}); 

Data in variables:

colStr0:
“Name,Count of Apps,Financials,#cspan,#cspan,Architecture,#cspan,#cspan,#cspan,#cspan,Mid-Range-Servers-PROD,#cspan,#cspan,#cspan,Mid-Range-Servers-ALL,#cspan,#cspan,#cspan,Storage,#cspan,Application,#cspan,#cspan,myCTO IncidentManagement,#cspan,#cspan

colStr1:
#rspan,#rspan,Total TCOA,Total Platform Cost,Total Storage Cost,% of Apps: Buy,% of Apps: Hold,% of Apps: Sell,% of Apps with DNP Tier 1,% of Buy/Hold Apps with DNP Tier 1,Linux/Solaris: count of servers prod,Windows count of servers prod,AIX count of servers prod,Mem/CPU Util: average % prod,Linux/Solaris: count of servers,Windows count of servers,AIX count of servers,Mem/CPU Util: average %,% Transformed Storage,% Utilization of Transformed Storage,AIT Retired YTD,AIT Decommissioned YTD,New Apps YTD,Count of Incidents,% Incidents caught by monitoring,Average TTR myCTO Incidents HH:MM”

colTypeStr:
“tree,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro,ro”

initialWidthStr:
“220,60,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,85,”

formData:"[{type: “settings”,position: “label-right”},{type: “checkbox”,label: “Financials”,value: “2”,checked: true},{type: “checkbox”,label: “Architecture”,value: “5”,checked: true},{type:“newcolumn”},{type: “checkbox”,label: “Mid-Range-Servers-PROD”,value: “10”,checked: true},{type: “checkbox”,label: “Mid-Range-Servers-ALL”,value: “14”,checked: true},{type:“newcolumn”},{type: “checkbox”,label: “Storage”,value: “18”,checked: true},{type: “checkbox”,label: “Application”,value: “20”,checked: true},{type:“newcolumn”},{type: “checkbox”,label: “myCTO IncidentManagement”,value: “23”,checked: true}]"

Unfortunately the issue cannot be reproduced locally.

If the problem still occurs for you, please, provide with a complete demo, where the issue can be reconstructed.
Here you can find a tutorial about creating a complete demo:
docs.dhtmlx.com/doku.php?id=othe … leted_demo