Hi Kishor. The conflicting plugin for the home page pagination issue was Simply Exclude, a plugin that excludes or includes taxonomies.
I still had the issue with category pages. Page 2 and 3 displayed "No Results Found" each time I selected the WP-PageNavi links.
I disabled all of my plugins, other than WP-PageNavi, and the pagination worked like a charm. I activated each plugin one-by-one, testing the pagination each time I enabled a plugin. To my dismay, the WordPress SEO by Yoast plugin was at fault.
My entire site is optimized through WordPress SEO! Fortunately, I discovered that by disabling a single plugin function, "Strip the category base (usually /category/ from category URL," my pagination worked and I could keep the SEO plugin activated. The option is located at Dashboard > SEO > Permalinks
But, what about the "category" path in my URL? I didn't want it there. I remembered that I used a plugin called "WP No Category Base - WPML compatible" that stripped "category" from my URLs. Fortunately, the plugin developer is active and the plugin is WP 3.4.1 compatible.
I installed and activated the plugin and surfed my site. End of story? Everything works and looks good!
I hope this helps.