Hmm, I don't remember ever having any problems with this not working as it should, but granted I've AFAIK always included both the global and per-project setting, since it was added many years ago. So, my guess is you've made a mistake then adding the option it to BOINC.

Make sure cc_config.xml is correctly named, and atleast under windows doesn't have a *.txt or something mixed-in.
Make sure cc_config.xml is placed in your BOINC Data-directory. Correct location is shown as start of the BOINC-startup.
Then making/editing cc_config.xml, use a bare-bone program like Notepad or similar, not a word-processor.
While the exact ordering in the file doesn't matter, it must still be placed within the <options>-part of the file. Example, you can have something like this:

<cc_config>
<options>
<max_file_xfers>1</max_file_xfers>
<max_file_xfers_per_project>1</max_file_xfers_per_project>
</options>
<log_flags>
<cpu_sched>1</cpu_sched>
<file_xfer_debug>1</file_xfer_debug>
</log_flags>
</cc_config>

Also check for any typing-errros.

To start using your updated cc_config.xml, just in BOINC Manager's advanced view choose the menu-option "Advanced, Read config file". While there are a couple options that only works on BOINC re-start, <max_file_xfers> and <max_file_xfers_per_project> is not one of them.

Note, if you decrease #transfers while some is actively uploading/downloading, it won't take effect immediately, but it won't start additional transfers except then allowed after the new settings.

Still uploading 2 at a time. Not sure what the deal is. All verified. No typing errors, edited with note pad on win7. Oh well.

Edit: looks like my ubuntu box is uploading 1 at a time. Watched my latest upload. Noticed uploads drop down to 33 Kbps on the big files. Not sure why. My windows box is still uploading 2 at a time.

Hmmm--

These past couple days, I've only had DDDT Phase 2 selected. I also have run other projects if selected project is not available. Last night, my PC downloaded a couple CEP2 WUs anyway. I thought this was an opt-in project. Maybe, if you've ever opted in to the project, that decision is remembered. It is not a problem for me, but it might be a problem for others. Even though I am still running only my old 2004 vintage Pentium 4 running XP, it does not seem to have problems with CEP-2, so personally, I like this behavior. (Yes, one of these days soon, I plan on getting a new PC).

Thanks for the tips!

Hi ibsteve2u,
thanks for the feedback - it is very useful for us. You said your result count went down - do you know whether the calcs run further than before instead, i.e., did they use to time out at the 12h mark and do they now tend to finish? If that is not the case, then HT may have been fine for your hardware and you could turn it back on again.
Thanks again and best wishes,
Your Harvard CEP team