When creating a conditional formatting rule using formula String such as:
ISNUMBER(SEARCH(ADDRESS(MATCH($C1,INDIRECT(HLOOKUP($B1,CategoryLookup,4,0)),0)+1,COLUMN(INDIRECT(HLOOKUP($B1,CategoryLookup,4,0))),4),$ref.E$1))

------------------------------Code snippet------------------------------
SheetConditionalFormatting sheetCF = sheet.getSheetConditionalFormatting();

ConditionalFormattingRule rule = sheetCF.createConditionalFormattingRule(
"ISNUMBER(SEARCH(ADDRESS(MATCH($C1,INDIRECT(HLOOKUP($B1,CategoryLookup,4,0)),0)+1,COLUMN(INDIRECT(HLOOKUP($B1,CategoryLookup,4,0))),4),$ref.E$1))");


PatternFormatting fill = rule.createPatternFormatting();
fill.setFillBackgroundColor( IndexedColors.YELLOW.index);
fill.setFillPattern( PatternFormatting.SOLID_FOREGROUND);

ConditionalFormattingRule[] cfRules = new ConditionalFormattingRule[] { rule };

CellRangeAddress[] regions = new CellRangeAddress[] { CellRangeAddress.valueOf( "D1:L10000") };

sheetCF.addConditionalFormatting( regions, cfRules);
----------------------------------------------------------------------

The formatting rule from the generated xslx file is written as follow:
ISNUMBER(SEARCH(ADDRESS(MATCH($C1,INDIRECT(HLOOKUP($B1,CategoryLookup,4,0)),0)+1,COLUMN(INDIRECT(HLOOKUP($B1,CategoryLookup,4,0))),4),$ref.e$1))

The problem seems to be reproducible with every mixed cell referencing; in this example $ref.e$1 , I attempted the other way around $ref.$E1 fixed column changing row same problem.
The fact that the Alpha index of the cell is lower cased is breaking it.