When you import contacts that are donors into the NPSP, there's a
NPSP Data Import Object that you want to import them into first after which you can run the Nonprofit Starter Pack Data Importer Tool which will create the accounts and households for you if it can't match them up to existing data.
For more on this I highly recommend you visit Import Data into Salesforce which has links to all the docs and a video on importing data into the NPSP. There's a template you want to use and other things you'll want to do. If you're not familiar with the NPSP, I also highly recommend you go through the two trailhead modules in the Manage Fundraising for NonProfits Trail.
In general, your best resource for NPSP questions is The Power of Us Hub. You need to be a registered User in an NPSP Org to access it.
NPSP updates itself automatically on a regular basis. If you check, you should be at least at ver 3.7 or above right now (not certain what release they're on see Which Version of Nonprofit Starter Pack Am I Using?). Apps like Appsona which are free to non-profits are best suited to importing data directly as they know how to handle this kind of data directly. It's possible you may have one of the triggers turned off or something like that. More than anything, the key thing for many orgs will be they
type of contact that's specified. If you click on the button that opens all of your Apps, you'll find a NPSP Setup Tab where all of the NPSP configuration settings are contained. There Nonprofit Starter Pack 3 Documentation will explain all of the settings and how to configure them particularly Manage Households, Organizations, Contacts, and Addresses.
Some orgs may have volunteers that aren't
donors. When that happens, an account may not be created for them, just a contact. Also, when an org has Corporate Sponsors or "Partners", they may have "related contacts" that don't fall under the household model, but instead are a child of the account for that Sponsor. It all depends on how your Org is configured. Those contacts would need to be configured to have that record type or be related to that particular account when imported.
The documents I referenced should help explain most of those things. This kind of missing information would also explain why it occurs intermittently for you. Again, I'd encourage you to get involved in the Power of Us Hub where you'll find a great community of very helpful and friendly people who are much more knowledgeable about these issues. I've stood up a number of smaller nonprofit orgs, plus done some pro-bono work, so only have a limited knowledge of all the NPSP pack's features compared to the pro's who are on the Hub.