I have checkboxes in my xslt file like this:

<xsl:element name="input">
<xsl:attribute name="type">checkbox</xsl:attribute>
<xsl:attribute name="name">
<xsl:value-of
select="$questionid"/>[1]</xsl:attribute>		
<xsl:attribute name="value">1</xsl:attribute>
<xsl:value-of select="QUERESPONE"/>
</xsl:element>
....
There are 5 more. The values of the checked boxes got
passed but for unchecked boxes I got "undefined
offset" when trying to get the values in PHP.

Is my code wrong?

Well, at a first glance it is unnecessary verbose. It could
be written in a more compact form:
 <input tyep="checkbox" name="{$questionid}[1]"
   value="1">QUERESPONE</input>

Assuming the variable $questionid holds the value "foo" this
would evaluate to
 <input tyep="checkbox" name="foo[1]" value="1">QUERESPONE</input>
which is unusual and probably illegal HTML (an input element should
be empty). At least, the widget name should not contain brackets,
which I suspect causes your problems with PHP later.

Solution: think *hard* how the HTML should look like, *then* write
a style sheet which produces the HTML (check carefully whether it
does), and only after this step go on with further processing of
the form values.