I responded to your original email, which I should have done initially.  Sorry 
for the back-and-forth on this.

On Aug 27, 2012, at 10:16 AM, Hans-Rudolf Hotz wrote:

> Hi Greg
> 
> Thank you very much for your e-mail
> 
> Unfortunately, we still see this behavior in
> "changeset:7404:ec29ce8e27a1" (July 20, 2012 release).
> 
> All screen shots in my original e-mail (21-Aug) were made with a server 
> running the July release.
> 
> Regards, Hans-Rudolf
> 
> 
> 
> On 08/27/2012 02:18 PM, Greg Von Kuster wrote:
>> Hello Hans-Rudolph,
>> 
>> If I remember correctly, the release in March did not properly handle the 
>> scenario where new tool entries were made within an existing section of the 
>> tool panel or new tool panel sections were added to specific locations of 
>> the tool panel.  In both these cases, the new entry (tool or tool section) 
>> were appended to the end of the section or panel rather than inserted into 
>> the desired location.  This is probably the cause of the behavior you are 
>> seeing.  This issue was corrected in the next Galaxy release after the March 
>> release.
>> 
>> Greg Von Kuster
>> 
>> 
>> On Aug 21, 2012, at 2:03 PM, Peter Cock wrote:
>> 
>>> On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>>>> HI
>>>> 
>>>> 
>>>> We have been struggling with this problem since we updated to
>>>> "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the
>>>> time to figure out whether it was a bug or whether we made a mistake.
>>>> Unfortunately, it now has reached a point where we have a serious problem
>>>> with our production server.
>>> 
>>> I saw something funny like your screenshot of the funny with labels
>>> on our machine when I last modified our tool XML file. It seemed to
>>> be caching something from the old XML...
>>> 
>>> Note so far we've not installed anything automatically from the toolshed
>>> (just manually). I've not dug into the issue - just mentioning this as a
>>> clue that this is probably not unique to your Galaxy installation.
>>> 
>>> Regards,
>>> 
>>> Peter
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>> 


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