Can you please show the full content of the rejection letter ? Yeah, from what I have read, you can do late-initial filing during this re-registration period. Maybe you need to indicate as such ?

Since you didn't file it the first time, now it's considered a Late Filing. You need to submit a letter along with the application showing the reason of late filing and you need to satisfy conditions below for late filing in addition to meeting all conditions for initial application.

From USCIS:
To qualify to file your initial TPS application late, you must meet at least one of the late initial filing conditions below:

During either the initial registration period of your country’s designation or during any subsequent initial registration period if your country was re-designated you met one of the following conditions, and you register while the condition still exists or within a 60-day period immediately following the expiration or termination of such condition
You were a nonimmigrant, were granted voluntary departure status, or any relief from removal
You had an application for change of status, adjustment of status, asylum, voluntary departure, or any relief from removal which was pending or subject to further review or appeal
You were a parolee or had a pending request for re-parole
You are a spouse of an individual who is currently eligible for TPS
OR

During either the initial registration period of your country’s designation or during any subsequent initial registration period if your country was re-designated you were a child of an individual who is currently eligible for TPS. There is no time limitation on filing if you meet this condition. So if your parent is currently eligible for TPS and you were his or her child (unmarried and under 21 years old) at any time during a TPS initial registration period for your country, you may still be eligible for late initial filing even if you are now over 21 years old or married. You may file during an extension of your TPS designated country.

Thank you for your helpful response... here is what i received.

could not see the uploaded document.

this is what's written there:
This is in reference to I-821, Application for Temporary Protected Status, you submitted. Your I-821, fees, and any supporting documentation is being returned to you for the following reasons:

To benefit from the provisions of the Temporary Protected Statius (TPS) Program, an applicant must file a complete application within the designated registration period. The TPS registration period under which you filed your application ended. Your application was postmarked after. Your application was untimely, and is therefore, rejected.

Please be sure you complete the application fully, submit the appropriate fees, and include all required supporting documentation.

Ny2, many thanks. another question, "You had an application for change of status,.. " this is one of the things in the rule.. how do i show this? I am currently in H1B which is valid through July 2017..

Those are "OR" I would suggest to go ahead with the Lat fine.
Send in Letters , bank doc, evidence of direct damage to home etc ...I think you should be fine with that.

More better consult with a lawyer