When you set up your conditional formatting, you will be pointing to a field in the repeating table and checking a condition.
So for example, you might have conditional formatting that says where [field1] [is not equal to] ["abc"]
This kind of formatting will only get the first row field1.
In the Select A Field Or Group dialog box, there's a "Select" drop-down box at the bottom... here you can choose "All occurrences of field1". This will look at all rows.
The XPath notation of the two conditions is as follows... you can see the difference:
Original: my:group1/my:group2/my:field1 != "a"
Correct: not(my:group1/my:group2/my:field1[. = "a"])