I have installed linux drivers for the network printer (am using Ubuntu 17.10). That translates to following steps:

wget http://download.brother.com/welcome/dlf006893/linux-brprinter-installer-2.2.0-1.gz
gunzip linux-brprinter-installer-*.*.*-*.gz
sudo bash linux-brprinter-installer-*.*.*-* MFC-L2700DW
 Answers: y y y y y A y
# The last y prints the test page successfully
# After it continues to installing the scanner 
# what isn't related to the question

This results in the printer showing up and the test page being printed successfully. The problem manifests itself when trying to print multiple pages.

For the following Duplex config in the driver:

~$ sudo grep -B 3 -A 5 DefaultDuplex /etc/cups/ppd/MFCL2700DW.ppd
*%=== Duplex ================================
*OpenUI *Duplex: PickOne
*OrderDependency: 25 AnySetup *Duplex
*DefaultDuplex: None
*Duplex DuplexTumble: " "
*Duplex DuplexNoTumble: " "
*Duplex None: " "
*CloseUI: *Duplex

I'm getting the following results:

wget http://delta-intkey.com/www/printtest.pdf
lp -o sides=two-sided-long-edge printtest.pdf -d MFCL2700DW
# Prints on both sides, long edge

lp printtest.pdf -d MFCL2700DW
lp -o sides=one-sided printtest.pdf -d MFCL2700DW
lp -o sides=two-sided-short-edge printtest.pdf -d MFCL2700DW
# All end up printing on both side, short edge

There was also an auto detected printer (assuming through Avahi or something):

$ sudo grep -B 3 -A 5 DefaultDuplex /etc/cups/ppd/Brother_MFC_L2700DW_series.ppd 
*CloseUI: *ColorModel
*OpenUI *Duplex/2-Sided Printing: PickOne
*OrderDependency: 10 AnySetup *Duplex
*DefaultDuplex: None
*Duplex None/Off (1-Sided): "<</Duplex false>>setpagedevice"
*Duplex DuplexNoTumble/Long-Edge (Portrait): "<</Duplex true/Tumble false>>setpagedevice"
*Duplex DuplexTumble/Short-Edge (Landscape): "<</Duplex true/Tumble true>>setpagedevice"
*CloseUI: *Duplex
*cupsBackSide: Normal

It behaves somewhat differently and take noticeably longer to start printing:

wget http://delta-intkey.com/www/printtest.pdf
lp -o sides=two-sided-long-edge printtest.pdf -d Brother_MFC_L2700DW_series
lp -o sides=two-sided-short-edge printtest.pdf -d Brother_MFC_L2700DW_series
# All end up printing on both side, short edge

lp printtest.pdf -d Brother_MFC_L2700DW_series
lp -o sides=one-sided printtest.pdf -d Brother_MFC_L2700DW_series
# Prints one page per sheet, no duplex

Any ideas on how to approach the problem?

You are reporting that settings between your Brother printer and CUPS are different and that printing is unusually slow, correct? You may be able to fix it by just correcting the differences between the Brother Printing settings and the CUPS settings.

Correcting Settings Differences

Someone else has reported being able to solve the issue of the two different sets of Printer Setting by this method:

Go to Printer Settings/Properties/Device/Two-Sided and that enables changing the duplex setting inherited from cups

If that does not help then I suggest you uninstall and try a new method of installing your printer drivers.

Correcting the Printer Driver Install

I am referencing this forum post. It refers to Ubuntu 8.04 but perhaps the solution could help you.

1. Completely uninstall all "brother" packages from synaptic (or apt-get purge [printer] [packages] [etc.]
   


2. Download driver (lpr & cupswrapper) from:
   http://support.brother.com/g/b/downloadlist.aspx?c=eu_ot&lang=en&prod=mfcl2700dw_us_eu_as&os=128
   


3. "sudo aa-complain cupsd" (something to do with AppArmor)


4. Ensure that /usr/share/cups/model exists. Make it if it doesn't.


5. turn on the printer and connect the USB cable. (may or may not be necessary if you're setting it up as a network printer).


6. Open the terminal and go to the directory where the drivers are.


7. Install LPR driver : "sudo dpkg -i --force-all [Name of the Printer driver].deb"


8. Install the cupswrapper driver: "sudo dpkg -i --force-all cupswrapper[Name of the Printer].deb"


9. Check if the LPR driver and cupswrapper driver are installed : "dpkg -l | grep Brother"


10. Configure your printer on the cups web interface


11. Open a web browser and go to http://localhost:631/printers.


12. 
    

    Click "Modify Printer" and set following parameters.

    
    
    

    Connection : "AppSocket/HP JetDirect"
    Device URI : lpd://(Your printer's IP address)/binary_p1
    Make : Brother
    Model / Provide PPD File : Choose the correct ppd file from /usr/share/cups/model
    

    
    

This last step is different than given by the Brother website, and makes all the difference.

Alternative Method for Setting up Drivers:

1. Turn off the printer and remove the printer under system/printing.


2. Open Synaptic and search for any Brother software. Then perform complete removal. (Potentially you may need to start over with a fresh install)


3. Reboot and go to Synaptic and do another search on Brother. You should have nothing installed. Then one at a time click on the cups files until you find your model. Mark for installation. It will auto add the correct lpr.


4. After installation switch the printer back on. It should be auto detected.

Additional References:

Perhaps this this post can help diagnose your issue.
Do not forget to also consult this wiki to troubleshoot issues with your CUPS on Ubuntu. I have also included the Arch Wiki on troubleshooting CUPS as the Arch Wiki tends to be pretty comprehensive.

Best of Luck!