This is the same outcome I had with a problem in 4.2.0 back in 2009:

https://groups.google.com/forum/#!searchin/spctools-discuss/xsltproc/spctools-discuss/47vHn08zLjU/7amlOxqjrCoJ

Maybe the problem, and fix is similar - I remember modifying the code to 
make it work, but don't have it handy to check back what I did. Don't have 
a 4.6.2 installation to check either. I will try to find out what I did...

On Monday, June 24, 2013 8:52:33 PM UTC-5, Christine wrote:
>
> Hi Luis,
>
> Thanks for your answer. Pls find attached 2 screenshots (default view, 
> only the 1st protein hit; and when "peptides hide" is checked, all protein 
> hits)  and web server error.log
> Let me know if you need something else.
>
> Regards,
>
> Christine
>
>
>
> Le mardi 25 juin 2013 11:33:27 UTC+10, Luis a écrit :
>>
>> Hello everyone,
>> Can you send us a couple of screenshots so we can see what you mean by "only 
>> display the first protein hit"?  I have not been able to replicate this in 
>> Windows or Linux.
>> Thanks,
>> --Luis
>>
>>
>>
>> On Mon, Jun 24, 2013 at 6:26 PM, <[email protected]> wrote:
>>
>>> Hi,
>>>
>>> same problem here with TPP4.6.2. Has anybody solved this?
>>>
>>> Thanks,
>>> Christine
>>>
>>> Le vendredi 15 février 2013 06:42:49 UTC+10, Brian Hampton a écrit :
>>>
>>>> Hi, 
>>>>
>>>> Using a Ubuntu install of TPP4.6.1 the ProtXML viewer will only display 
>>>> the first protein hit from an iProphet result.  However, I discovered 
>>>> today 
>>>> that if I check "hide" for peptides, then it displays the entire result 
>>>> set.  It will export to Excel the results with any setting.
>>>>
>>>> Maybe this clue will help troubleshoot for a solution..
>>>>
>>>> Thanks in advance,
>>>>
>>>> Brian
>>>>
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