Very surprised that it works for you, because it should not. 
I found out that xalan:component and xalan:script extensions for XSLTC
actually are not supported:
http://xml.apache.org/xalan-j/extensions_xsltc.html (Constraints section).

Can you please tell me how do you programmatically invoke the transformation
in your code?

For now, I found the way to static or instance methods of Java classes. This
is an acceptbale solution because I can do probably everything I hoped to
achive through xalan:script and more. 
Example:
<xsl:stylesheet  version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform";
               xmlns:clarus="xalan://clarus.TestXsl"
extension-element-prefixes="clarus">
           
<xsl:import href="HorizontalRow.xsl"/>
<xsl:output method="html" />

<xsl:template match="/">
    <xsl:variable name="something" select="clarus:new()"/>
    <xsl:value-of select="clarus:testFunction(.)" />
...

where clarus.TestXsl is my own Java class.

As for you comments.
Of course, I used the xml file that Xalan provides. I also tried to pass
hardcoded parameter to the function - still does not work.
This:
<xsl:template match="/"> 
   <p><my-ext:timelapse multiplier="2"/>We have logged your enquiry and will 
      respond by <xsl:value-of select="my-ext:getdate('5')"/>
   .</p> 
   Some other text
</xsl:template> 

gives me the result:

<p>We have logged your enquiry and will respond by

Of course, if I comment out the xalan:script function invokation, the output
is as expected.

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