Issue with .htaccess

Hi Team,

I have been facing one strange issue with .htacess

In Permalink i have set the structure to post-name and with this option .htaccess generated is :

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

Now the issue is, earlier everything was working fine but recently i am facing 500 Internal Server Error, not everytime but whenever i tried to delete more than 3 posts or try to upload a csv with only 50 records in it. Also i have been getting “Service Unavailable” message every now and then.

Now while troubleshooting i tried everything but nothing helped then i checked with my hosting provider (godaddy) after hours they updated me that my .htaccess is creating issue and asked to change Permalink structure to Default, i tried changing the same and .htaccess generated with this option is below :-

# BEGIN WordPress

# END WordPress

After this i tried to the tasks on which i was getting 500 error but to my surprise now everything was working, now i was able to delete upto 200 posts and i was able to upload a csv with 250 records.

Just to double check i rolled back the Permalink structure to Post Name and again the same issue started.

Please suggest what could be possible reason and how can i sort it out by keeping permalink to Post Name.

PFB other details :-

Server :- Godaddy (Shared) Unlimited Bandwidth and Space.
WP version :- 4.5.2
Theme :- CouponXL 3.7

Thanks,
Vineet Sharma