There is almost certainly a gap in the [x2]APIC ids on your processor, meaning that some value of the APIC ids don't map to any logical processors. You should use the 0xB leaf of cpuid to find out. You can look at the reference Intel code and algorithm (https://software.intel.com/en-us/articles/intel-64-architecture-processor-topology-enumeration/) for the steps, but it broils down to calling with EAX=0xB, ECX=0 and obtaining in EBX the number of logical processors (threads) per core and then calling cpuid again with EAX=0xB, ECX=1 and getting in EBX the number of logical processors per processor package.
The old method of using leaf 0x1 cannot account for APIC id gaps. Alas that's the sample code still given on the MSDN Visual C++ 2013 reference page (http://msdn.microsoft.com/en-us/library/hskdteyh.aspx), and it is incorrect for processors made in 2010 and thereafter, as you found out whether by using the code from MSDN or similarly incorrect code from elsewhere. The Wikipedia page on cpuid, which I've recently updated after struggling myself to understand the issue, now has a worked out example in the section on "Intel thread/core and cache topology" for enumerating topology on a processor with APIC id gaps, with additional details, including how to determine which bits of the APIC ids are actually used and which are "dead".
Given the code sample currently offered by Microsoft on their __cpuid() page, this is basically the same question as Logical CPU count return 16 instead of 4 because it's rooted in the same interpretation error of the Intel specs. As an explanation for MSDN's poor show, the code they offer worked okay before 2010 or so; Intel used to provide a similar method before the x2APIC was introduced as you can see in this old video/article: https://software.intel.com/en-us/articles/hyper-threading-technology-and-multi-core-processor-detection If you look at the various versions of the MSDN page on __cpuid, their code sample has basically remained the same since 2008...
As for the single hyperthreaded detection bit, that is a longer story, already answered by me at Why does Hyper-threading get reported as supported on processors without it?. The nutshell is that that rather legacy bit tells you if the processor package supports more than one logical processor, be it via hypethreading or multi-core technology. The name of the bit is thus rather misleading.
Also, I suggest changing the title of you question to "Using CPUID to detect CPU topology, reliable solution?" because I've found your question completely by accident. I was searching for Sandy Bridge cpuid dumps on google when I found your question.
