Eventually I mitigated the problem by downloading the files manually from data.astrometry.net.

So, just for further reference if anyone encounters the same problem, here is the procedure to download the index files manually.

1. Use a FOV calculator (or ask Ekos to solve an image using ONLINE astrometry.net) to determine your FOV.
2. Once the FOV is determined, the automatic downloader in Ekos will tell you which index files are required and recommended for your setup.
3a. Go to data.astrometry.net/4100/ and data.astrometry.net/4200/ to download the required/recommended files. Make sure these are moved to /usr/share/astrometry (sudo may be required if doing this via command line). OR
3b. Visit www.stellarmate.com/support/ekos/align.html and download all the corresponding.deb files which are associated with the index files desired. After that, install them in one go with the following command

sudo dpkg -i astrometry-data-*.deb