@Kristian_Andersen and @arambaut, thank you very much for your inputs.
Attached are the XMLs, Trees and Log files (zip format) generated while running Beast 1.10 and Beast 2.5.1 with similar parameters (whenever possible). After all, the low ESS issues were specifically related to ‘treeHeight’ and skyline population parameters (popSize and groupSize).
Beast1 files (after 90 Mchains):
beast1.10_zikv-India.zip (2.1 MB)
Beast2 files (after 100 Mchains):
beast2.5.1_zikv-India.zip (2.2 MB)